Personally, I think the anti-lefty bias (at catcher and in the infield) is just an example of baseball sticking with a tradition despite any real reason to support it. The usual justification for avoiding lefty catchers is, as noted above, that they would have trouble the owning out runners when there's a righty in the batters box. But if that were the case, wouldn't righty catchers be at a disadvantage when a lefty is batting? If so, is think teams would steal a lot more when a lefty hitter is up, and that doesn't seem to be the case.
As for infielders, I'm told the problem is that a lefty has to pivot before throwing to first base, and that I costs them a fraction of a second to do that. But it seems to me if there was a talented fielder, he could make up for that delay with quick footwork and hands. I don't think there's any legitimate reason not to allow lefties to play these positions.