I've recently left a gym after 3 years because of a similar issue. I love sparring, and I've learned a lot about myself by facing a big fear of getting hit in the head when I first started training. I've taken some big head shots but it's always been an accidental clash with a lot of apologizing and such afterwards. I'm an extremely small female so I often have to ask people to speed it up just a little bit because they're afraid of hurting me.
Unfortunately, I started having seizures (completely unrelated to Muay Thai)in December last year, right before a trip to Thailand with a potential fight lined up. I still wanted sparring time to keep my skills up but couldn't have head contact for 6 months. Everyone at my gym was so understanding and very cognizant of my injury; I didn't get hit in the head once.
I still went to Thailand with my main training partner and my teacher. We've had an agreement: no head shots thrown at me, but I can throw at them. Now, I don't know exactly why this happened and can't get an explanation out of them other than "it wasn't malicious", but I ended up getting hit repeatedly in the head by my partner and kicked in the head by my teacher. I'm not sure if they were frustrated with me, if I was sparring too hard and they wanted to get me to slow down. We were supposed to be going 20% but it felt like they were thrown much harder. The article Sylvie wrote on sparring perception definitely rang true for me at that moment because there isn't a precise, objective way of knowing why it happened. To say the least, I left that gym!