Hey Gotcha!
first of all, regarding comets: they are mostly composed of water with a few small bits of rocks/ dust inside. as long as the hiigarans chose comets with minimal rocks/dust, the vast majority of the comet should evaporate in re-entry long before it hits the ground. Of course, this method, if used too much (and yes, chuking an entire ocean's worth of comets do indeed fall within the "too much category") would heat atmosphere a small amount. However, with a little luck, that much water vapor in the upper atmosphere should also serve to block a significant amount of the sun's rays, reflecting them back into deep space and canceling the heating effect on the planet somewhat. ultimately, I'm much more sure about the viability of this method than even the Hydrogen + Oxygen method, primarily because the latter requires so much shipping that it would be incredibly difficult or take incredibly long period of time to accomplish. (transporting enough hydrogen to make an ocean? lol.)
Secondly, regarding the Skaal: While I admit that it is possible, it is also (according to the wiki anyways) highly unlikely.
"With the beginning of the Exile, the entire surviving Hiigaran population was forced to board a convoy of transports that would ferry the Hiigarans through space
until a suitable homeworld could be found for them to resettle themselves on. For generations, the convoy ventured into deep space, and eventually, the Hiigarans as a race were virtually forgotten. During the journey, the Hiigarans suffered miserably and soon lost their sense of identity. Many of them did not survive the journey due to the primitive technology employed by the convoy, leading to the loss of many vessels and their passengers. Despite the hardship,
the Hiigarans eventually found refuge on the desert world of Kharak, where the Hiigarans found a place to call home and reestablished themselves as the Kushan."
http://homeworld.wikia.com/wiki/The_Exilejudging from the lines bolded above, its more than likely that the the hiigarans didn't even know that kharak existed before stumbling into it.