No. They shouldn't ignore politics, especially not in such controversial times where more than ever the people must speak up.
Marvel employees and the Marvel work community is allowed to have opinions, you know, and if someone stops reading Marvel because Marvel have a less than favorable opinion of Trump, and based upon Marvel's past statements and Trump's low approval rating already this will be the case, it wouldn't hurt Marvel at all as millions upon millions more will still watch their movies and many will still read their books.
After all, look at Saturday Night Live. They made fun of all politicians and are rightly pointing out the hypocrisy of politicians and using their own words against them. Many Trump supporters say they have sworn off SNL yet despite that SNL viewership hasn't been this high in a long time and their ratings are up. Did they take a risk on angering Trump fans? Yes. Did it pay off? Of course, and it'll pay off for Marvel as right now talking about Trump and his antics, even if it angers Trump fans, is where the money is. While badmouthing Obama wasn't really profitable or popular outside Fox News.
Heck, Eminem declared that he would work to bankrupt Trump, Trump fans are furious and swore off his products yet now Eminem is at a high in popularity and his profits are up.
So don't expect Marvel to hold back against such a big target as Trump when the money is there.