It seems like a reasonable idea. One is supposed to get to know your faction before you go jumping in to Capital Ships. Forced play time with the appropriate regular ID may work some what. We'll have more people flying capital ships that at least have some experience flying that faction under their belt.
However, I do see several problems with this idea. Such as existing faction members wanting to create new characters. This will lengthen the set up time for all characters significantly. Or maybe it won't -- 3 hours flying with an ID is ample time to spend repping your guard IFF. We can't simply stop people from gaining guard IFF until they have a certain time either, because remember Guard systems all start as hostile and you need to rep to neutral before you can enter, and at least full neutral to buy certain fighter equipment. This way, only Guard ID purchase would be able to be restricted by time.
A lot of debate is required to sort this idea out, as it stands now I don't believe it will be a change for the good.