Yes, if Barclay was a woman that would be equally as problematic for her to create sexual versions of her co-workers.
No, you’re forgetting that he kissed Troi. How much more sexual would it have to be in order for it to be a clear sexual component on an early 90s family friendly show?
I found this short interview with Sarah Higley (aka Sally Caves) that sheds some light on how she came up with the idea and what her thinking was. She doesn’t specifically mention her thoughts on Barclay recreating a sexualized version of Troi, but the bit with the script in the beginning of the video seems to at least confirm that she wrote her into the script (as opposed to it being introduced into the script at a later stage by Michael Piller or someone else from the TNG writing staff).
Listening to her it sounds to me like she was merely looking at the holodeck as a way to visualize someone’s private fantasies and didn’t consider the implications of recreating real people in humiliating or sexualized ways.
The difference of course being that Barclay didn’t just fantasize about a co-worker (like Bashir), but went so far as to create a sexualized facsimile of her. I don’t think there’s anyone here who wants to say it’s problematic to have sexual fantasies.