So what? Take that out, and its like bowling with the bumpers in the gutters to keep the little kids from rolling straight gutter balls. You might as well just go all the way and turn on god mode. What you're talking about is downgrading Shadowrun from an R to a PG rating.
As for flashbangs, you can houserule them to not do chunky salsa, but under the rules, they're no different from other grenades.
The thing is, you're trying to baby the PCs too much, Michael. Am I saying toss grenades every chance you get? Of course not. But there's no reason to take it easy on them. Play the NPCs like beings with intelligence and training appropriate to their stats, instead of mooks to be mowed down by the PCs. Sometimes this means that the PCs will die horribly, and you might not even get in the door. Hell, in one of the adventures in Corporate Intrigue, some of the suggested security measures before you even get in to fight the elite MCT guards and the technomancer cyborgs are things like monowire strung between landscaping, 'flowers' that spray Seven-7, and pop-up LMGs with ExEx ammo. Welcome to the Zero Zone.
Play your NPCs realistically. If a grenade going off isn't going to wreck the place (or endanger those containers with the biohazard markings, etc.), then throw a grenade if they have them, and they don't care about live prisoners. If it gets to the point where the PCs are having a stand-up fight, instead of firing on the move as they try to get the hell out of dodge, then they've already lost. Even the Pink Mohawk crowd emphasizes overwhelming the enemy as quick as possible. Also remember that the force the enemy brings to bear will reflect what the opposition is using. If you have a troll with dual LMGs, six combat drones, and a mage who's summoning high force fire spirits, then yes, throw the grenades. If the players are using silenced weapons and stealth tactics, then grenades are a 'last resort' weapon, or possibly a dead man's switch.