Discrimination against theists by atheists in academia
Addressing the question in the context of the Unites States, it appears that it's questionable that any discrimination, and that if there is any such discrimination, it is a) not particularly strong, and b) highly entangled with other factors, such as conservative religious social and cultural activism.

It is an undisputed fact that in the United States there is a higher percentage of non-believers in academia than in society at large.  The key and unresolved question is whether this is a result of self-selection (e.g., non-belief being correlated with interest in scholarly investigation as a career and belief being correlated with disinterest) or whether there is also some component of discrimination.  One can find serious and respectable scholarly work both arguing that there is significant bias and that there is no significant bias.

Even articles strongly advocating that bias exists, however, find that if any such exists it is not particularly strong (else it would not be so equivocal to study) and that it appears to be measurable only with respect to religious people who are a) strongly culturally conservative, and b) activists with respect to politically polarizing positions (e.g., opposition abortion, gay marriage), and also c) at very particular stages of career (entry to graduate school, possibly at tenure promotion).

In short: even amongst those studying and debating the question, it appears that even if any systematic bias exists in US academia, the vast majority of theists are not significantly affected.