Backend dapps without graphical client(Alethzero, Mist, etc)

Hi,
Borja from Traity here.
We recently started to play with Ethereum and are really excited about what this platform will be able to achieve. We have started working on decentralizing our reputation platform but there is one thing that worries us.
We want to create Ethereum accounts for each of our users and potentially would like to generate transactions and send messages on their behalf. The reason for that is that we can't expect they use a specific graphical client like Alethzero, at least from the very beginning. So, our initial approach would be to use the headless client with the json-rpc api enabled and create the accounts and therefore the keys for them(although the api right now does not allow accounts creation nor deletion)
So, our first concern here is that we are not completely sure if this approach would scale as apparently all the keys are stored locally in the client machine and we are not sure if it is in the roadmap an option to add external datastorage for the keys because it won't considered a real necessity.
We are aware that the idea behind Ethereum is to be as decentralized as possible so the backend apps should not be necessary at all as long as the applications can be run within Solidity contracts, but we are worried if this point of view would leave other possible applications out or even if forcing the user to download a specific browser would mean too much friction for the standard user and would affect to the Ethereum adoption