Only been playing for about a week but I have to agree that there is something amiss when a Combine player goes out o his way to build two unit types; Snipers, and Headcrabs (via the Launcher).
A simple nerf would to be reduce the range, making their use more of a defensive measure, and not an optimal one (however, an upgrade for elite/sniper combine units could be 'scent masking' making Zombies ignore them). This lets the player who chooses to go with Headcrab canisters make them a more risky and require a dedicated rush strategy, while letting a player who wants to turtle to get late game units/Striders have a last ditch defensive option.
A complex nerf would be to make the energy cost vary based on closeness to a Citadel. The nearer they are the closer to 50 energy a canister costs (yes that's a reduction). I'm not sure what the numbers would be but this could be balanced, perhaps, to make their advanced deployment as a weapon much more complex. I don't know if the code exists for this, it's a suggestion, that's all.
An unpleasant nerf would be to make there be an increasing % chance the more times you fire a canister that it 1. misses, 2. blows up the launcher and spawns lots of headcrabs at the launcher. No idea what the #s should be on this, but an increased # of headcrabs spawning at a launcher blown up due to a miss-fire seems appropriate. This I think would be the most dramatic way to punish a player who insists on building 5+ launchers (I've seen it, and I've been on teams where players do it and I don't like to see it happen
) ... which leads me to my next suggestion. Four building based suggestions. I kind of prefer these because they should cut down on the spam building that I'm seeing which I think is most problematic.
1. The launcher is a component of the mechanical bay, the cost could be similar, but this building is usually too valuable too risk building far out from the base. By incorporating the launcher into it (as an upgrade first, and then an ability to launch the canisters) you also make it a part of the mid-late game.
2. Canister launchers can only be build 1p/Power Generator, the player can see a link, but this effectively increases their cost as a forward deployment, cuts down on spam building marginally, but keeps their defensive utility in tack. Coupled with a reduction in range (say 70% of current range) this might work as a compromise of different suggestions.
3. Personally I think the best thing to do is to limit the canister launching to being an ability of the Citadel. Keep the range, or make it more a component of development (supply increase, increases the range of canister launching marginally). Increase the cool-down to 12 - # of supply stations held. Now the canister spam is going to happen only if the Rebels did not do their job of taking supply stations early, and will be limited by # of canisters by the number of Combine on a team. You could also have an option at the citadel of "spawning head-crabs" at the citadel as a latch ditch defense effort. I like this because the big impact is that you can not use headcrabs to advance/assault unless it's a small map which people will know about ahead of time.
A final suggestion.
4. That radar tower the rebels can build. An upgrade you can purchase from it, creates a circular zone of interference which can not be launched into. This is something I think you may want to try to implement, before other changes. I think it adds some strength to the rebels mid-game.