Like GrimmLAN13 said, the easiest way to do this is to not summon any allied troops to help you throughout the final quest.
Though if you want to use your troops, there is a way to keep them alive. You just need to level them up. The emissaries at your camp /do/ serve a purpose, and when give the correct items, will level your troops up.
* Golems - are at max level and don't require any items (4 troops, lvl 15)
* Werewolves - are at max level and don't require any items (16 toops, lvl 12)
Dalish - Elfroots, deep mushrooms, metal shards, deathroots - Max troops 50 + Max lvl 9 - 10 xp per item
Redcliffe - Money - Max troops 50 + Max lvl 7 - 10 xp for 50 silver; 42 xp for 2 sovereigns; 225 xp for 10 sovereigns; 750 xp for 30 sovereigns
Dwarves - Sapphires, Amethysts, Malachites, Topazes - Max troops 50 + Max lvl 9 - 10 xp per gem
Mages - Runes (no grandmasters) - Max troops 12 + Max lvl 10 - 10 xp per rune
Templars - Runes (no grandmasters) - Max troops 16 + Max lvl 12 - 10 xp per rune
There is no good way to tell if your troops have been leveled up. Some people like to go by what the emissaries say after you've deposited items, but it's not conclusive.
(some info taken from the da wiki)