I'll second (3rd? 4th?) the annoyance with atheists (especially the New Atheists,) and I say that as an atheist myself. I'm not annoyed at their "fundamentalism" (I'm not sure what's meant by that) but by the fact that they're so often tone-deaf to real issues of inequality and suffering (case in point, Dawkins constantly putting his foot in his mouth re: feminism.)
Atheists who've embraced humanism and feminism, on the other hand, I tend to get along with great.
Clarifying, since you asked. Fundamentalism is traditionally defined as a literal, strict, and legalistic interpretation of scripture. It brooks no questions, no discussion, no doubts, and no deviation. "But wait," you say, "atheism has no gods, and ergo no scripture." Well, I'm getting to that part. I define fundamentalism somewhat more loosely. Reason being, if you look for a scriptural basis for much fundamentalist belief, it's either a huge stretch based on massive amounts of cherrypicking and reinterpretation, or it's just made up; in either case, it has no relation to scripture. So, in much the same way that Westboro Baptist Church, the Klan, ISIS, and others pick and choose their scripture to have a retroactive "godly" rationale for their reprehensible actions, so too do the New Atheists turn scripture of any sort (with the occasional exception of some Buddhist texts) into a strawman that bears little relation to faith as it's currently practiced. Moreover, like their other fundamentalist brethren, the New Atheists don't just (dis)believe in God; instead, you must disbelieve as completely, and in the same fashion, that they do (there's no hell, admittedly... just varying levels of juvenile snark and mockery). Likewise, they brook no argument, true discussion, or disagreement. Religion is evil, period, and must be eradicated.
Islam, of course, gets a "special" dispensation, since Harris, Dawkins an Hitchens (plus their ideological hangers-on) would like to see not only the religion but also its practitioners wiped out... in which respect, they're more like the Christians they'd otherwise be looking down their noses at than they'd care to admit. After all, fundamentalism makes strange bedfellows.
All of which is a long-ish way of saying, believe what you want, or don't, or doubt*, and I have no issue with you. But when you insist that others believe, or disbelieve, as you do, that's where I take issue.
*I think that whether you believe or not, agnosticism is a more reasonable approach than the certainty that goes with either theism or atheism, but that's a whole 'nother discussion, and this probably isn't the place for it.
Back to the comic:
The person who would be the most chill about it would be Dale, obviously. Because Dale is chill about everything. Almost everything, anyway.
The person I think would be most likely to say something unintentionally hurtful out of sheer obliviousness? Marigold. And I think Dale would not be chill about that. Nor would Momo. Or May, I expect. I can imagine all three of them giving Marigold a stern lecture about respecting other people.
Aside from a couple of times when he's been more direct than usual with May, have we seen an instance in which Dale wasn't chill? I can't think of any.
Regarding Marigold: I think you'd be right on the money if the situation played out that way, but I get the feeling that Jeph is trying to avoid having the comic go in that direction, letting the human characters' usual "be good to each other" message carry the day. I think that the Anthro-PC characters are his stand-ins for the times that he wants to explore things that get closer to actual rights issues (and blatant dick jokes).