My son's school would put a child in isolation if they turned up having been drawn on with Sharpie, and the parents unable to get it off, purely to try to prevent that child from being bullied by their peers. It's got absolutely nothing to do, I suspect, with the fact that the child was a victim of a "prank" - but to prevent them from being the victim of their fellow students...
OP, I think you did your best to handle it responsibly, and like another PP, I can see why your ex is precisely that. I know, from bitter experience, what it's like to be belittled in front of your 12 year old son by the other side of their DNA - and, take heart; your son might resent the way your ex speaks to you, and be taking absolutely no notice of what his father had to say on the matter.
Regardless of what some posters on here have been spouting... it does equate to assault. The boys who were scribbled upon? Did not give their consent, were upset by the outcome of their "friends" behaviour, and one has been subject to ridicule by his school friends at a sporting event (not to mention, from what has been said, told off by a teacher for something that was beyond his control!). 12 and 11 year old boys are not only old enough to know better - but old enough to be held accountable (and no; I'm not one of "those parents" who would go running to the police... but I am one of those parents who would be explaining in no uncertain terms to my son what might happen if he were to be stupidly irresponsible enough to allow something like that to happen to someone he considers friend enough to invite them into his home overnight!). There has to be a line somewhere, because in a few short years, those boys will be sharing their sleeping space(s) with young women - and consent is consent, irrespective of whether it's an 11/12 year old boy, or an 18/19+ year old woman.
I'd be livid if my son came home from a sleepover looking like this (and he's 14, so his ability to be stupid is at an all-level high, given that teenagers simply don't think about consequences to their actions until it's too late). I'd be grateful to the OP for having tried her utmost to (a) get the Sharpie off my son's face, and (b) told her son/the others how ludicrously stupid they were and to think if there's ever a next time... but for my son? If he were friends with the OP's son? There wouldn't be a next time. I'd not want to run the risk of a repeat art session with my sleeping son the canvas, or... and this is the crucial point... something worse happening to him when he was at his most vulnerable (ie, asleep). That would stand for a sleepover at the OP's house, and at mine.
When I was a teenager, back in the distant ages of darkness, I had mixed sleepovers - girls and boys all huddled in our individual sleeping bags, at 14, 15, 16 years old, watching horror films and verbally mocking one another. Maybe we were boring, but at least we were simply tired the following day, not sporting bushy Sharpie'd eyebrows or glasses... My 14 year old son has been to one sleepover - and he came home with a bloodied nose where his "best friend" had deliberately kicked him in the face. He never went back to that "best friend"'s house, and my son phased him out of his life, through his own choice. OP... sad as this might be, the choice which your son made to cave into peer pressure, may well have cost him two friendships. And if I were you? I'd be very loathe to have my son spend much time with those boys who pressurised him into either joining in with them, or allowing them to humiliate two vulnerable boys in a space that their parents obviously believed they'd be fully safe in.
I'd also understand that the parent who reported back to say that their son might have to suffer repercusions for your son's actions... is actually pretty darned angry with you and your son. Be prepared for them to distance themselves and their son from you and yours, regardless of how well you actually handled the experience.
