I've already been working on v0.10 (April release). For April I'm trying to add more things for the player to do in space and make existing activities more fun and interesting. I already added the ability to set a specific ship as a target and your turret will automatically fire on that target. This reduces friendly fire but doesn't stop it.
I've thought of several ways to solve friendly fire but each one has a big impact on how the game is played. It could just be a checkbox on the Station Menu. Or ships could have non-weapon equipment slots where you could slot upgrades such as a faction targeting computer that won't damage a specific faction. Finally it could also be built into the weapon itself so that some weapons don't hit a specific faction.
The time required to build this really depends on how I decide to make it work. For instance, building a whole new equippable upgrades system is a lot of work. So, I'm not sure I'll have a solution in time for the April release but I've definitely been thinking about it!