If you don't need them for breeding immediately you could sell them and wait until you get better (large) habitats for that type of dragon. You can buy them again when you need them, but no sense in losing your only pure Earth if you're going to have to buy another one soon.
Generally I'm willing to lose the quick-hatching dragons like Plant and Lightning, but remember Earth dragons take forever to hatch. Since you get one extra habitat every level, after level 10 it's really no big deal to keep just one of every basic type, but there's no reason to keep more than one.
I try to always keep one of each dragon around in the Hibernation Cave you can unlock at level 14. Immediate access to these dragons can help when there's a limited time dragon you want to breed NOW, that way there's no re-hatching dragons before you can start breeding.