Free up the memory of pruned species by deleting hidden references from TemplateReaction objects

Objgraph shows after pruning, the pruned species are still in the memory so not too much memory is retrieved. And it is because there're still some objects (mainly from TemplateReaction objects in Re, see the pic below) referring to them. After deleting those objects, memory was eventually released.
![in function prune prunedspecies-7-objgraph-aftfpruned](https://cloud.githubusercontent.com/assets/2739496/4926366/e74733ca-6532-11e4-98c9-24ac007fb110.jpg)