Normally, I'd advocate saving RP for skins only, since anything else can be purchased with IP.
However, Rune pages have a massive IP cost, which limits purchases of champions and, more importantly, the runes you need to fill the pages.
The only exception I've ever made to my IP/RP purchase rules has been for rune pages - I've never used my RP for champions, boosts, or anything else other then skins(and rune pages). And I have to say, the rune pages have been some of the best purchases I've ever made.
So yes, they're definitely worth it. Two rune pages are not enough - nine aren't perfect either, but they'll massively increase your flexibility, and are infinitely better then two.