My hip had been bothering me for a couple months (pinching and discomfort on squats). I decided to to some trap bar deadlift with a slightly higher load a couple weeks ago and strained my hip flexor. Apparently, sitting at a desk all day is really bad for your hips. It was enough that I struggled to get dressed the next morning due to the pain.
I decided enough was enough and mad a PT appointment. Luckily, the PT office recently went through some barbell training workshops and are offering me complimentary barbell training to go along with the physical therapy I'm doing. Seems to be getting better but haven't done any lower body exercises until things get healed up.
Ortho's, chiro's and PT's are cheering on all those who promote and want everyone to continue squats, deads and any lower body free weight work as they age.
So unless you are trying to win a Mr. Universe contest, or your way of living requires you to squat with weight......I would look into the many other ways to keep your lower body in shape.
And if what you are doing now with your PT doesn't yield results......try having your lower/middle back checked. Just because your back isn't hurting doesn't mean it isn't jacking your hips.