A tricky mission, that requires a lot of micro-management at times. Not too hard though with a good strategy.
My strategy for Mission 11: Cleansing
The overall focus in order of importance:
There are two ways to do this:
A. 1. Spam Hornets and only protect the Hornet spawn buildings.
2. Station the Hornets at the Flood spawn points and have them take out the flood buildings quickly.
3. Wait for the cleansing beam, and eliminate most of the Flood if not all in one pass.
B. 1. Spam Turrets and station your troops to protect the turrets and the buildings.
2. Gradually build up your Hornet force and take out the flood buildings in between cleansing waves.
3. Build Turrets everywhere and eventually win.
Being a 'safe' play style, I never really tried "A", however I'm almost positive it would work on this mission as long as you kept some Hornets(or the Spartans) in reserve to clean off the Flood drop pods.
My general walkthrough steps:
For Strategy B:
1. Immediately divide your forces to the four corners of the North deck area, and a couple troops on the raised deck area to the South.
2. Station them so that they can hit the flood that come up the walls and land.
3. Focus on building as many turrets as possible, and balancing between anti-infantry and anti-air upgrades on the Turrets.
4. Once you have a lot of Turrets going up, including on the raised deck area in the middle, then start building Hornets.
5. Station the Hornets to help out the various defense points.
6. Get some reserve Hornets and start taking out the Flood factories.
7. Try to take out the side Flood first if possible--and leave at least one Hornet at least Flood location as you go so they can take out the respawning Flood buildings.
8. Keep building Hornets and building/repairing Turrets when you can.
9. Try to have both sides clear by the time the first cleansing beam comes through, then take out the North flood spawns, build Turrets there(with Anti-Air), and leave a couple Hornets up there.
10. Mass attack the South flood, taking out the Flood 'Stone Throwers' first! Station some troops there so they don't respawn, and wait for the next cleansing wave.
11. You're done!
Sentinels will keep spawning throughout this mission, and are harmless until after the first cleansing wave--then they will start attacking you also, and particularly wrecking your Turrets. Keep an eye out and keep rebuilding Turrets.