Using the blockchain for providing other services, besides bitcoin transactions
There are already tons of services doing this, so probably worth focusing your creative efforts elsewhere. Here are the ones we know about on Coin Secrets:


Proof of Existence
BlockSign
Stampd
La Preuve
Bitproof
Stampery
ProveBit


As for pruning, assuming you use the same OP_RETURN mechanism as these tools, then they may be pruned by some nodes. But I imagine there will always be plenty of full archives of the blockchain available (even if this is eventually a paid-for service) so I doubt that your timestamped hashes will ever be truly lost.