I'd probably try the reaction without a protecting group on a test scale to see if it is really necessary to protect it. How basic are the conditions going to be? It would help if you can give more info on the next step, but I realise you may not be in a position to do so.
I've tried a benzenesulfonyl protecting group to no avail
Does this mean the protection step failed, or that the following step failed as a result of the protecting group?
but I'm wondering are there any other good protecting groups for the NH that won't affect so much the reactivity of the 7-aza?
Electron withdrawing PGs (like sulfonamides, carbamates etc.) will probably significantly alter the electronics of the system due to their conjugation with the indole N lone pair. While this may not translate to a problem (depending on the next step), perhaps an alkyl group (e.g. Bn) would behave more similarly to the unprotected compound?