LB – I wrote my last post before seeing your last post. That does make things better.
But what I wrote still stands. Are there other things that bother you about the shul? Can you find a shul that it is clearly acceptable?
I would also suggest approaching the Rabbi politely and asking him about the parts of the Chumash that bothered you. When you hear how he responds, you will have a better idea of what his approach is. He might tell you that he wasn’t aware of those references and he is shocked by it. He might tell you that he is aware that those Chumashim are problematic but he inherited the Shul and it wasn’t something he was able to change since there were more important changes to make. Or he might laugh off the problem.
Whichever response you get, it should tell you what you want to know about the Rabbi and about the shul.