There seem to be two main mentalities players have when approaching the enemies: the "I need to clear out this entire room" approach and the "I'm going to save mana and dodge my way across the room" approach. I'd say most of us do a mix of both, with some people favoring one and some people favoring the other.
Some people are just not going to be entirely satisfied until the room has been cleared. People want to be able to "complete" a room before moving on to the next one. There's a sense of accomplishment in that, and some gamers really thrive on it. It's also good for players who like a somewhat slower, more exploration-focused style of play, and thus want to clear out spawners as they go so that they don't feel rushed by the constant onslaught of enemies. Now that enemy spawners can be destroyed, these players are going to feel compelled to take the time to clear them out as they go through a room. This is a boring and tedious activity, and many players will get frustrated and grudgingly change their playstyle. It's probably not going to ruin the experience for many people, but they would probably have more fun if they were able to play the way they wanted.
So why not let them? Would anything really be lost from the game if spawners worked on a "spawn once on each room entry" basis?
Players who want the satisfaction of clearing a room before moving on would be able to do so and enjoy it. Players who don't care about clearing a room, and prefer to strategically dodge past the enemies to save resources would have the same experience they have now - since they're not killing the enemies anyway, it wouldn't matter whether or not the enemies came back after death.
Let's look at an example of a very simple and common situation.http://i.imgur.com/qLalI.jpg
Assume everything works as it does now. We have a player, an item the player wants, an enemy that wants to kill the player, and an enemy spawner. Here's what I imagine the two extreme player mentalities would do:
Player A - Hop over the approaching enemy and grab the item. Wait a moment, then hop over the enemy again and exit the room. Practical and efficient. Nothing wrong with that.
Player B - Attack and kill the enemy, then grab the item. Out of a desire to feel that the room has been "cleared", run over to the enemy spawner and spend several seconds blasting it until it is destroyed. A somewhat more practical player might instead kill the enemy, grab the item, and quickly leave the room before another spawns. Either way, this is not ideal for this player.
Now let's imagine that the enemy spawner isn't there, just the lone enemy. How does each player approach the room now.
Player A - Hop over the approaching enemy and grab the item. Wait a moment, then hop over the enemy again and exit the room. This experience is unchanged and still enjoyable.
Player B - Attack and kill the enemy, then grab the item. Take another look around the room to make sure that nothing has been missed, then leave through the door. Now we have a sense of accomplishment and satisfaction for this player.
To be clear, I do not think that the room should remain clear into the future. Should either player decide to return to this room later, they would find that the enemy has returned, and they can then choose how to deal with it again. And I suspect that many players will actually tend to dodge the enemy on later visits. This is how I play games like Zelda and Metroid - the first time I enter a room, I take the time to fully explore the area, smash every crate, and kill every enemy. When I pass through the room again later on, I'm happy to ignore many of the enemies, as I have already mentally mapped the room; it has been "cleared" in my mind, even though there is now a fresh supply of enemies in it. But without being able to clear it out on that first visit, I would not have as enjoyable of an experience.
And again, none of this applies to boss rooms, which can justifiably feature an endless stream of lesser enemies to contribute to the fight.
So, my proposal again: Make enemy spawners invincible and invisible, but have them only spawn one enemy when the player enters the room. The spawner is then deactivated until the next time the player enters the room, at which point the room is repopulated with a fresh batch of enemies.
If that seems like too dramatic of a change, here's an alternative: Leave everything the way it is now, but let enemy spawners be destroyed by a single melee attack (but they still regenerate when the area is reloaded). I'm having a hard time thinking of a downside to this!