In general, yes, tenure protects you from retaliation for anything you say, write, research, etc. That is the point of it. But the instructor still has to teach his/her course. If this is going on in a math course, then a complaint could come about not teaching math.
But in a biology course, the person could probably make a case that they are teaching biology, even when they are actually rejecting science and its underlying principles.
The student also has academic freedom, I'll point out, so speaking out against a creationist professor should never result in any sanction. That, unfortunately, is harder to guarantee.
Another issue, of course, is whether the instructor is requiring students to adopt anti-scientific positions for any reason. You can't attack a person for their religious beliefs, of course, and under tenure you can't attack them for speaking about those beliefs, but you can require that they not try to undermine the beliefs of others.
One effective way to counter ineffective teachers is to avoid them. If that isn't really possible then complaints to the dean, etc. or letters to the editor, etc. are certainly possible. But be aware that you are very unlikely to change the minds of people who choose to ignore science using any argument whatever. There is some research, in fact, that arguing with such people only deepens their belief.
From the Dean's standpoint, while he/she may not be able to fire a misbehaving teacher for what they say, there is no reason for the Dean to be required to let that person anywhere near students, or promote them, or give them raises, etc.
Finally, in some (but sadly not all) places, the other faculty can provide helpful peer-pressure against instructors who use their classroom time to proselytize rather than teach.