Suppose there’s a reputable organization that is non-profit, and any precedes it receives goes straight to the needy. Basically, it is pure charity. The needy are very thankful for this organization and many people regard this organization as a wonderful help not only to the needy, but to the community as a whole. However, this organization supports a philosophy—and it even has an agenda—that goes against your personal beliefs. It isn’t just something that you find a unique quirk. The agenda is so bad, that you find it morally abhorrent. On the one hand, donating resources to the charity helps the community; on the other hand, you will indirectly support their agenda which is morally abhorrent. What should you do?
The Problems of Love from Sartre and Beauvoir to Irigaray
Shaun Miller's Ideas 
It sounds like what the Mafia use to do with their community housing projects. Positive behaviors can be used as a front for disguising another agenda. Maybe like a Potemkin Village. I couldn’t support something that at face value does good, but has a morally abhorrent force driving it.
Find a different charity that is helping those same people in need. There are always plenty of options.
The answer depends on the consequences of supporting the organization, so framing it as an “agenda vs. consequences” split doesn’t make sense if we’re interested in a consequentialist answer — the agenda is part of the consequences. Will the donation raise their profile and enable them to spread their agenda more effectively? Will other people know I’ve donated to them and think less of me? What other unexpected consequences might there be from many people supporting a charity with repugnant views?
If the increase in their public profile is minimal, and the effectiveness of their charity is the largest available return on investment, I think we would have an obligation to donate to them while hoping that a group with a better agenda comes along soon.