If you cannot get assistance from the airlines in advance I would politely repeat my story to the gate agent when you arrive at the departure gate. We have flown a couple of times with my friends family....she has 2 DS's with a syndrome that is similar to autism. Both times she got the boys situated at the gate and then told the agent what the situation was and how important it was to be seated together...when she explained that they might be quite annoying to other passengers if seated solo they were only too happy to rearrange a little....
Kind of like the time I was travelling with my 4 year old daughter and the flight was full, our connection late and no one wanted to move (we were the last ones to board)...and the 2 remaining seats were 6 or seven rows apart....so I calmly plopped her in a seat next to a man in a $900 suit, got out the snack bag, found the gummy worms and reminded her not to put her sticky hands on the nice mans clothes, then I got the sippy cup out and pulled the lid off and told her to ask for GRAPE juice when the nice drink lady came by (by this time he is bobbing around trying to find another empty seat) and then I pulled out a big bag of markers and a coloring book and told her if she ran out of pages to color maybe she could use some of that mans papers (he had been flipping through some huge report when we arrived), and because he still hadn't offered to move I told him not to worry if she cried for the first 20 minutes or so of the flight, she'd quit sooner or later....at that he leapt out of his seat and RAN to the other open spot...I honestly think he would have thrown himself out of the plane onto the tarmac if another seat had not been available!!
Just make it sound like you are doing everyone a big favor to sit by your own child and they'll move!!