What should I do after advisor got upset when I expressed "belief in evolution" and then said he couldn't add me to his research team?
Well, this is clearly not a match made in heaven.  (Sorry, I really didn't intend this as a pun.)  What a shame, you had really bad luck.

There is no need to keep this a secret from the other professors.  It is very unlikely that they are clones of this guy, even if they do have a friendship with him.

Yes, you do need to talk to the dean of graduate studies in your department and let him or her know what happened.

I don't think that particular research team would be a healthy place for you.  The guy behaved badly.  You need an advisor you can trust to act like a mensch.

In terms of the effect on your future studies -- I can't say.  If you can find another advisor you want to work with at your current institution, great; otherwise, you might want to go elsewhere.

By the way, do you mind my asking, why aren't you in a PhD program?  In physics it seems a bit unusual to be in a Master's only program.

(Just so you know, what he did was illegal in the U.S.  I'm sure the dean of graduate studies in your department will know that, and I'm not going to suggest you mention it; but I wanted you to know, so you will see this clearly as THE PROFESSOR'S problem, not yours.)

-- Edited to add: for some info about the illegality of this sort of thing, in the U.S., see the U.S. Department of Justice's intro page: http://www.justice.gov/crt/combating-religious-discrimination-and-protecting-religious-freedom-20