So, the question is whether you can put an aftermarket keyless remote start system on your Rogue. Yes, you can. Will it void the warranty on the Rogue? Only if that starter system can be attributed to a failure that happens on the Rogue.
Dealers often send vehicles out to local aftermarket shops for moonroofs and keyless remote start systems, even alarms. Get some other quotes from local shops to make sure your quote isn't just a low ball one. And check with your dealer that they weren't going to install the Nissan one, but rather an aftermarket one.
Though, I have to ask, in this day of high gas prices, why waste fuel by running the vehicle prior to getting to it and going?