I think the letter is insensitive, and the issue has been badly handled. No gold stars for your Head in Communication Skills 
Personally, I would expect a phone call from our school (and would definitely have had one) over something like this - and a discussion about what was going wrong, not an assumption. Parents and teachers ideally working as a team.
Little girl in dd's Y2 class (she's 6) had soiling issues this year. She is definitely not trying to get off school, she has had sluggish bowel problems since birth - and when stressed, or dehydrated, obviously it gets worse. She was so embarrassed she tried not telling anyone, putting up with the smell and childrens' comments until home time 
Her Mum went in to school, talked to the teacher, who was lovely. They worked together to make sure the girl felt able to tell her TA, who would give her a hand cleaning herself up (ie be around to make sure she was ok, not do it all for her). They also worked together to encourage the girl to drink a lot more (which she was refusing to do for her Mum, but did happily for teacher of course!). She's only had one accident since then, and is a lot, lot happier.
That was a good example of school and home working together for the good of the child.
What a shame your ds's school doesn't know how to initiate this, OP - but perhaps you could try and be the one to kickstart an improvement there? Deep breath, and rather than the complaints form (even though you're entitled, imo), ask for an appointment and talk calmly to the Head or class teacher, with letter from doctor in hand, about how best to support your ds with this issue. They need to know he has a medical condition, they need to know he must be allowed the toilet at any time, and that he must drink lots of water.
Good luck 