Atheists & Agnostics

If this person has been your SO for so many years it seems you'd have a strong emotional attachment to them. Cutting ties as some have suggested seems extreme and a waste of a years long emotional investment.

I'd suggest you share clearly how much you value this person and how important they are in your life. Then support them, no not the decision to join a cult, but them as an independent person.
Then set boundaries. Explain your lack of belief and your reasons for it. Explain that you will not accept proselytizing or whatever thing that you find unacceptable. But remain open to conversation and show a willingness to listen and answer any questions they have.

Be careful of ridicule, snark, or being dismissive. Your SO might take it personally and become defensive. In that vein it's probably a bad idea to be aggressive against this church or your SO's new friends. Treat them with kindness as respect as well, even as you explain you don't respect their beliefs.

Consider educating yourself on apologetic (the defense of the faith) and anti-apologetic.
Don't preach, be kind, be the SO that your partner deserves.