What do the chargers get me? 6 mercs who get utterly destroyed by a small Venetori ambush.
What do the Qunari get me? Thedas's version of the CIA and US navy. Seriously, you get one of the best spy networks and THE most powerful naval force in the friggin world.
The Qunari are jerks? Well, Joseph Stalin was a jerk as well but the US teamed up with him anyways and sent him TONS of equipment and money in the fight against Nazi Germany. That alliance ended up playing a very critical role in Germany's downfall. Sometimes, its better to not be picky about your allies in the middle of a war. Oh and to all of the people saying that the Qunari do not honour alliances, Bull pretty much says that this alliance is a big new step for the Qunari. They've apparently never made a deal like this with a foreign power before. Whether or not they will invade Thedas one day is a different question but for the time being, this alliance offers valuable support in the fight against Cory. Cory is the immediate threat that needs to be dealt with. Why not get some Qunari aid? Even if they do attack Thedas in the future, why not use them to our advantage while we can? Think of them as tools rather than as allies if you must.
Except the strategic situation is different. Corypheus isn't a direct threat to the qunari, and the Inquisition has been doing rather well in containing him so far (for me, this quest has been coming up after both the Winter Palace and Adamant Fortress). Which means that any scenario where I take a hit to save qunari forces benefits them a great deal more than it benefits me.
If the WWII scenario applied, Corypheus would be on his way to defeat the qunari, and by supporting them I'd bind his forces so that he'll have fewer resources to oppose my own attack. Instead, you can accurately predict that an alliance with the qunari would not take a significant weight off your shoulders, since they're not positioned to aid you in time even if they wanted. Instead, the net outcome is that you strengthen them at your expense with little gain for yourself. Of course the qunari are interested in such an arrangement...
Edit:
Or you can look at it from the qunari side: by allying with the Inquisition the Inquisition *may* gain a little benefit, but we have an additional foot in the door with no expense on our side, and if the Inquisition takes losses saving our people it'll be easier to conquer them in the future.
Nope. I won't be the one letting the qunari gain a foothold. Not with my main Inquisitor anyway, who is also a mage who has allied with the mages and has even more reason to detest the Qun.