How are you supposed to guarantee they stay apart? That sounds near impossible.
I would just move the desks far apart, make sure they were always in seperate groups, and try to physically seperate them. But if they gravitate to one another during free times that is rather tough to deal with.
When I was a camp counselor I had one boy in my group whose mother did not want him to play with a little girl in another group. The two had developed a 'puppy love' for each other and the Boy's mom was horrified by his crush. She felt it was inappropriate for him to say he liked a girl. They were 7 & 6 and just liked playing together, they never caused trouble... just looked forward to playing at the end of the day. Since she was in a different group the only time of day we even saw this girl was at free time at the end of the day.
I told the mom I would try to keep them apart when our groups shared activities but I couldn't make guarantees. Before heading to free play at the end of the day (since I only had one kid in my group) I would pull Z aside and remind him of his Mom's request. I would also remind him that I would give her honest reports... but the self control to stay away had to be all him. Sometimes they still played together and I felt horrible for the both of them because they had been great buddies. Mom was peeved I didn't physically pry them apart of give Z a time-out for playing with the girl. I had to explain several times that I reminded Z of her requests, but if they weren't misbehaving I could not punish Z.
If I had both in my group it would have been impossible. I could not *tell* one kid in my group to totally ignore another. Especially if they wanted to be together! You can seperate desks, keep them in different groups for group activites, and try your hardest.... but it must be on the Mom to tell the Boy not to play with XYZ kid and up to the boy to exhibit the self control. The most you can do is *try* to seperate and give honest reports to Mom who can impose whatever consequences she likes on her son.