Can a non-person have “qualms” about something?

I agree with @Robusto that there is nothing wrong with anthropomorphizing the theory in this manner. You could also say

This theory makes no bones about challenging everything that physicists believe to be true.

It's metaphorical, especially anthropomorphizing, usage. It is not appropriate (it is somewhat semantically jarring) in literal language, for example in technical writing.

In expository discourse it could work but with some other reinforcing usage of 'theory' as an individual. Still, you might want to reword, to emphasize that it is the -proponents- of the theory that have no qualms.

Suggestions for alternatives, that preserve the intention and syntax but not the exact meaning are:

This theory has no restrictions in challenging...

This theory has no limits in challenging...

This is a literary device known as the pathetic fallacy, in which human emotions or motivations are ascribed to inanimate objects. Great writers down the ages have used it.