Yes they have a point in that we who practice a spiritual teaching would benefit from asking our self deep question about our way of practicing, and about our way of understanding the teaching.
It is the one who practice that is the one who should ask themselves the questions for gaining deeper wisdom.
In my understanding, when a non practitioner of a religion ask negative questions, it is not for learning but to get the practitioner to fail and "admit" that maybe e his or her spiritual belief is bad or wrong
But you don't have to see the other person in that way to learn from him or her and not just the answers from your (a spiritual person's) own questions. Unless your knowledge depends on other people's reactions and comments, unless the other person doesn't want to talk about it, there should (in my opinion) be some curiosity of how said religion is seen negatively and the points that other person is making "without needing" to go by their intentions (not all have the intent you mentioned).
If I asked you why did god tell people to murder women and children and how wrong that is of god to do, what can you learn from this-from me-that won't hinder your bias by what you think my intentions would be?
Enlightened people don't sit on a cushion asking themselves questions. Most religions have some sort of interaction with people who see their religion both negatively and/or positively. There's a consensus of something to learn and love within that other person (or enlightenment) that they can reach and the enlightened person can be there to one day trigger "their" experiences.
How do spiritual experiences excuse negativity from other people who belittle religion if not taking their intentions (if you were to guess without asking) as a decision factor?