As far as I know it doesn't have any permanent influence. You do get an extra 100 points on your SeeD Exam (although probably at the cost of some points for time remaining), a lot of AP and IIRC an Orihalcon.

Killing the thing is easy if you grind a bit beforehand. All you need is Quezacotl's Med-Magic RF (the one that transforms regular spells to -ra spells) and a bunch of Thunder to convert to Thundara. Then draw some Double from Elvoret and you're good to go. Just don't forget that you cannot kill it on your very first encounter.