I should start by saying that I do believe Bonds used steroids, and that technically no one has proven he did use them. I will cling to that technicality for as long as I can, because I am an unabashed Barry fan and a proponent of "innocent until proven guilty". Though I realize that for many, the evidence is already strong enough to prove him guilty. This is all beside the point, though.
What if Barry hadn't started using steroids? What if he went his whole career without a single injection, balm, or pill? A pure, unenhanced player among many who were decidedly not.
The general consensus seems to be that Barry started using steroids sometime in the mid-nineties, possibly as late as 2000. His career with the Pirates is generally considered steroid-free, but almost all of his Giants campaigns would then have been partially PED driven.
Let's start with some milestones. Without steroids, I don't think he would have broken the single-season home run record. I think his single-season home run totals would drop for every season. But they would still be good. I doubt he'd lose more than ten home runs a season at maximum. Definitely no more than 100 over the course of his 14-year Giants career.
In total, I think he drops maybe sixty bombs and finishes around 700 at the end of the 2007 season. Remember, when he got to San Francisco he was still under thirty and had two 30+ HR campaigns in the last two years. I also don't think his intentional walk totals or OBP would suffer much; he wasn't being walked a lot until 2002, and not a ridiculous amount until 2004. But that 2004 team wasn't the offensive juggernaut previous seasons had produced, so I think other teams would have walked him anyway just because it was easier to pitch around him than let his still-prodigious power and undiminished, incredible batting eye hurt them. I'd say he loses some average as well, since he's not hitting them out with such frequency, but not much. His stolen base totals would probably increase, since he's getting more chances to run the bases with fewer balls leaving the yard.
But this still leaves him as probably the most iconic, powerful slugger in the game. Bonds was so utterly dominant that he could afford to lose those home runs and still be far-and-away the best hitter in the majors. So he still gets called to the witness stand in 2003. He still has to answer the questions about whether he used steroids; there would be no real evidence this time, particularly in regard to his head size, but I highly doubt the grand jury would ignore him just because there wasn't any evidence. They would at least want to talk to him.
This time, of course, he can categorically deny everything since he definitely hasn't used steroids. No obstruction of justice here; he can give clear and complete answers to any questions the grand jury might have.
Would it matter? Would the grand jury believe him? Would they still launch an investigation? I think they absolutely would. I think the clear nature of his answers would light a new fire underneath them; if they can prove anything, they've obviously got him on perjury charges. They don't have to prove that he said he didn't use steroids and that he used steroids, just the last part. The court case becomes easier; it's finding the evidence that will be impossible.
So I think he still gets at least investigated. I'm not sure if he gets tried; I think Ilston would have thrown the case out due to lack of evidence. But he still doesn't get signed after 2007; after being investigated and MLB wanting to keep him out as a token of the steroid era, he hits free agency without breaking Aaron's record (though he passes Ruth). Despite no trial, I think his career ends after the '07 season, this time for absolutely no reason.
What about the media? Do they still attack him and accuse him endlessly? Of course. It's never been only about the steroids with Bonds; he's been singled out because he's the best. If the media just cared about steroid users, then Bonds and steroids would have been more of a local story than a national one; local media would focus on their team's users. The Red Sox' writers wouldn't care about Bonds. And even without steroids, Bonds is probably still the best hitter in the game.
Jeff Bagwell is the other reason I believe this. Bagwell has no connection to steroids at all. There's pretty much no chance he was using. He's got Hall of Fame numbers. But the question remains: will he get in? Bagwell was a HOF player who wasn't using when everyone else was. So people assume he did. Or at the very least they aren't sure, and tend to give some credence to rumor. It's just a case of steroid era+good player = steroid user.
Bagwell wasn't the best player in the game, even if Bonds is removed from the equation entirely. And since I think Bonds would have been the best without steroids, there's no chance he isn't associated anyway. If Bagwell can see his HOF chances at least diminished for no reason other than rumor, Bonds absolutely is assumed to be a user. After all, what sportswriter can resist the obvious idea that since Bonds is better than steroid users, he must be on something himself? It's easily written, since you don't have any sources to talk to, it's sensationalist, it's about the best player on any field.
So without using, I think Bonds is still tagged as enhanced. His disdain for the media and their reaction to that is just pushing him towards the obvious end. I think it would be more speculation and less "look at the size of his head!" but I doubt many writers would go from convinced to unconvinced. They would just assume, as they have with Bagwell, that everyone was doing it so he was too, and his league-leading numbers wouldn't have helped him. For the same reasons, his HOF chances would have been marginalized to the degree that I think he wouldn't have gotten in on the first ballot.
That's really the sad irony to all of this. If Bonds hadn't used, he probably would've been the best player in the game for awhile anyway. He probably would have led the league in several categories - instead of pretty much all of them - for several seasons. That would have fueled the steroid suspicions. And the steroid suspicions would have, for a while at least, kept him out of the Hall. Had he hit worse, actually diminished his case for entry, then maybe he would get in sooner, as fewer voters would be convinced he was a user. This whole ethical judgment of players in the steroid era has led me to the resoundingly idiotic conclusion that a player would have a better chance of getting in if he hit worse, and that's all that needs to be said.