It's ok if they are little boys because maybe they feel safer going to girls restrooms where there is less of a chance of getting raped. A lot of people I know do this with their younger children, and if they are out with their fathers, the dads wait outside the restroom, letting the females know that they are waiting for their son, not creeping.
In addition to completely usable family restrooms, mothers frequently bring their sons into the women's restrooms if they are uncomfortable going into men's restrooms alone, and if a boy is with his father, there is no reason in the world Dad can't take a field trip to a family restroom or take his son into the men's restroom. I would also like to see what reference you have for an increased risk of sexual assault as a young boy in a male restroom, because actually EVERYONE who is raped, sexually assaulted, or molested is significantly more likely to be victimized by someone they know personally than by a stranger...
1. Boys should NOT allowed into the Girls' restrooms at school.
2. Boys should be allowed in the WOMANS' restroom as long as their mother is present, but not allowed without a female guardian.
3. Just bring them into the Mens' restroom with their father, it's really not that difficult.