While it is more realistic to play this way it feels like it unbalances things, at least in my Campaigns. The typical result is a situation where I'm just racking up extra kills and salvage. I use the BV method as well as killing off a Locust and leaving a Warhammer undamaged is just too easy. I calculate the full BV of the enemy so main plus reinforcements.
It does unbalance things a bit, but like you said, more realistic. I strive for as much realism as possible (why I have vehicles and crews that never see combat).
As for when to do it, I usually stick around the listed number, though BV does have a play in my head about it. If it was a matter of just taking out Lights and the other half being Heavies, I wouldn't make that call. Balanced is probably the best case to use. I've had 'sandpaper' battles where both sides had severely reduced BV's but few actual kills. I've also had battles where I was bull rushed by hovers and paper-armored lights who died in droves yet barely made a dent in the enemy BV. Obviously, battles like those skew the system.
I also tend to 'put myself in the enemies head'. Would I be worried about accomplishing the mission if that were my force? If you take them down to 49% but you're at 51% and in a bad spot (out of ammo, blew initiative, etc) Would they just automatically give up? Don't shackle yourself with one hard, fast rule. Look at each one separately.