Eh, I think if he aligned with KO and Zayn and screwed over AJ he would be booed.
I know it's very unlikely but there have been a lot of teases of tension between DB and Shane, maybe I'm just reading way too much in to it but you never know what WWE is thinking sometimes.
They could do it just to prove they can
You are reading too much into it. The dissension was there for storyline. I'm assuming it was done so that there'd be 'justification' for firing Bryan when his contract expired and he left the company. Now that he's cleared, that's obviously done with. They got him new merchandise, he's reportedly single-handedly pushed Wrestlemania to within 1000 tickets of being sold out after they were struggling badly to sell tickets, the first episode of Smackdown after he was cleared drew the biggest rating since the Smackdown after Wrestlemania 11 months ago.
There's also no reason for him to align with KO and Zayn. He fired them, they ambushed him, he flat out said he was going to kick their ass at Wrestlemania.
On another note, they already tried to turn him heel when fans wanted to cheer for him: when they forced him into The Wyatt Family. It failed.