The question really should be “what is the alternative”? Your choices are
1. Don’t make any programs for non-frum Jews so we do not run the risk of engaging goyim in kiruv
2. Do extensive background checks to ensure everyone in your program is halachicly Jewish.
3. Have a “liberal” open policy and try to bring in as many Jews as possible. If at some point you realize someone is not halachicly Jewish then you work from there.
Answer # 1 is the same as giving up on your Jewish brethren
Answer # 2 is very impractical and will do more harm than good
Answer # 3 seems like the only way.
Let’s say there was a cattle car of Jews going to Auschwitz every day and you could save the entire group (with some risk) although not everyone is a halachic Jew, would you do it?