We should, if the something in question is destructive, immoral, or contrary to the public good. We don't have to tolerate every possible opinion just because some people are conflict-avoidant.
Also, a commit's author should be judged from his code quality, not from his opinion on random issues.
You say that, but there's been a number of OS developers that have been ostracised and expelled from communities by something they (for example) tweeted. Contributors are rejected to contribute because they don't conform to a code of conduct. People lose jobs over being called out for jokes at conferences (and over calling out said jokes, both in part thanks to internet armies).
So while in theory it should, in practice people will get vetted and judged for their online presence.
In other words, the ye olde adage is still valid; don't be identifiable online. If you're an OS developer / contributor with an unpopular opinion, best to keep that part separate from your OS contributor profile. And keep your real name safe.
Is it really true that for no combination of position and person, it's a net negative for that person to consider the merits of that position?
For example, should a recovering alcoholic consider an argument regarding one particular liquor being better than another?
I don't care if my coworker thinks that gay marriage is a sin. It is his right to hold that opinion. If he doesn't let it come in the way of his work it's fine. But that doesn't mean I am asking everybody to consider his viewpoint. If it is absurd enough for you you needn't worry about it.