The pilots could report that they are having technical difficulties and are unable to override the current route programmed into the autopilot. They are also have issues disengaging the autopilot. So they are "forced" to continue their flight on their pre-filed flight plan.
Any direction from ATC would be replied with "Unable":
* https://www.boldmethod.com/blog/lists/2021/01/10-times-you-s...
* https://aviation.stackexchange.com/questions/7915/who-has-th...
* https://aviation.stackexchange.com/questions/24756/when-can-...
* https://atccommunication.com/cannot-comply-with-an-atc-clear...
Short of shooting down the plane there's nothing anyone can do about it.
So repercussions tend to range from nothing, through wagging fingers, slaps on the wrist, to sanctions, UN resolutions, UN-sanctioned wars, or if you really piss someone off, non-sanctioned wars.
I don’t think Belarus will be invaded, and I guess Russia would veto any particularly nasty move in the UN, so really this leaves stern words and some unilateral sanctions against the Lukshenko regime. Doesn’t seem like overwhelming penalty (though well-targeted and enforced sanctions can bite quite badly).