ORIGINAL: Lobster
Perhaps that could be better represented by a lower proficiency level rather than hamstringing the whole Soviet Army.
Perhaps...but it seems that giving the whole Soviet Army the ability to freely coordinate among its various armies in 1941 would be giving it an ability that it simply didn't have.
There were some Rifle Divisions that had upwards of 65% veterans of the campaigns from the Winter War and since. So to paint the entire Army with one broad stroke doesn't seem accurate.
Certainly some Soviet units were pretty decent, even the crappy ones fought fanatically under the right circumstances. But I think that the issue with granting them "free support" is whether all of those units--army wide--should be able to join in coordinated attacks rather than how good each individual unit was. One of the Red Army's biggest problems in 1941 was their inability to coordinate operations between armies (and to a lesser extent, within armies).
Rather than replicating the effect of transferring units around, I believe that the main effect of giving all Soviet rifle divisions (all units?) Free Support would be to make the Red Army as a whole a much more coordinated and effective organization that it was in fact (certainly in 1941, less so later). This could be pretty potent once the Soviet units had built up some proficiency. Meanwhile, at least initially, individual Soviet units would be less effective than they should be because of their lowered initial proficiency.
Sticking the entire Army with lower cooperation levels is a one and done solution. No way to recover from it.
That's true, but it is one of many limitations imposed by the game engine.
I wouldn't say that your proposed approach is "wrong", it just fixes one problem and introduces another. Anyway, if this is the approach that you find appropriate, go for it, address it in the designer's notes, and be done with it.
One other approach to consider would be to dispense with armies altogether and put all divisions within fronts (ie, TOAW formations would be fronts rather than armies) and allow units to cooperate with all units within their front. I would argue that this is actually how Soviet fronts operated later in the war (late '42-early '43?); while it wouldn't be especially historical in 1941, it might be a compromise solution to consider.