With Force Commander, Tarksus and Avitus at your disposal I recommend to use tactics described below.
1. Avitus leads the squad and when enemy appears within sight order him to set up the gun.
2. Thaddeus follows close behind Avitus
3a. If the enemy gets within Avistus' range wait for them to get pinned, then order Thaddeus to jump into the group - this will eliminate most of the enemies and knockdown or scare off the rest.
3b. If the enemies won't come close enough try luring them with Thaddeus (either by just moving ahead or jumping into the enemy group provided it's not too large). Then, the battle should proceed like in 3a.
3c. If you don't have Thaddeus make Tarkus do the luring - his grenades are quite impressive against large groups of enemies.
4. Tarkus and Force Commander should support Avitus in pinning down the enemies and dealing with the toughest enemies (as they can be equipped with energy weapons, flamethrowers and rocket launchers early on).
IMPORTANT: during the missions later in game you will encounter enemies equipped with rocket launchers and some kind of mortars. Those units have an incredibly long range and should be dealt with using Thaddeus jumping in the middle of the crowd using hit and run strategy.
What SHOULDN'T you do?
1. Avoid open areas so that you won't get surrounded.
2. Conserve your grenades - try to save as much as you can for the last minutes of the mission when you will be faced with some kind of a tough enemy.
3. Avoid taking Cyrus for your missions, despite his obvious pros he cannot match Thaddeus' jet packs, Avistus' heavy bolter or Tarkus and his accuracy.
Forcing enemies out of the building.
There are a few ways of doing that - you can attack the building with conventional weapons (the enemies inside will die sooner or later), throw in some grenades (not recommended, as you should conserve your grenades), torch the building using flamethrowers or use the explosives. You can also call in the artillery support, but that would be a waste.