the wording on the force choke card says choose a non-commander, non-operative enemy trooper mini, is that reffering to the original rank of the unit or to the rank that may have been assigned to them by a card/ability effect.

If i promote a Corps trooper unit to commander when the commander dies, can the heavy be force choked off that unit?

No they become immune to force choke in this instance.

From page 27 of the RRG:

A unit that has been promoted to commander does not retain its previous rank. It is considered to be a commander for all effects and game play purposes.

1 hour ago, 5particus said:

If i promote a Corps trooper unit to commander when the commander dies, can the heavy be force choked off that unit?

Doesn't even have to be because the commander died. Say you bring Cassian as your commander, but then use his Covert Ops ability, which makes him an Operative instead. Your army must have a nominated commander, so you could nominate a Mandalorian Resistance unit as your new commander, making them immune to Force Choke and any other ability that cannot affect Commanders.