For me, balance is lost when one 'side' dominates regardless of whether it's legal or not. I take a look at MtG for example. Those that played back in 2004 will remember this bad boy:
For those that played in the standard format, every deck was either a)playing affinity or b)playing to stop affinity. There was no in-between; if you didn't do a or b, you had no chance to be competitive.
The same should hold true to other games. I haven't played an MMORPG since Everquest so I won't comment on that aspect, but for RtS, it is relatively the same. Most RtS follows a paper-rock-scissor concept: i.e. Grunts > Archers > Dragons > Grunts.... I understand that that's a simple example but the general scheme overall is the same.
However, when one strategy effectively dominates the scene then it becomes necessary. When WC3 first came out burrow rushing was a dominate game play strategy among orc players which went to the highest level. The same with undeads summoning multiple graveyards and using necromancers to send, literally, an endless army of skeletons to attack the enemy.
On a large or major game no one player can ever be in a position to make a decision to say that a certain skill, ability, strategy, etc is a dominate strategy. You can play 10 or 50 games a day and it won't matter when there are hundreds of thousands of games played everyday. The developer or whoever has access to see the results of all these games are the ones that are in a position to make the educated decision of whether something needs to be changed or not.
Good players I know don't really care about changes, it simply means it's time for them to find a new way to be the best. Players that overly rely on a fixed planned are the real gripers about because they can't adopt the change.
The only thing that would give me pause is that any changes inevitability leads to unintended results. Changing ability X might put an immediate stop to a issue at hand but who knows what other consequences it might face down the line? No amount of playtesting can ever detect any and all bugs in a given system especially given how large the scale of today's games are.