Your client rulers eventually die off and the allied democracy remains. It's okay to have a client ruler in place for a while, because you need one with high influence points to convert the province to your culture. That's the only way you're ever going to expand in earnest. Otherwise the further you expand, the greater the trouble you will have with public order. You need to convert provinces to at least 50% Western Mediterranean polities if you ever want them to behave instead of rioting and rebelling without a governor.
Also, yes, you can destroy allied governments and rebuild them with newly recruited client rulers. Doing so obviously disrupts or delays the ability to recruit troops from that province. Also, yes, the client rulers count as family members, so if you recruit a lot of them you might experience problems as I did with demographics and new children being born or women getting married off to potential male suitors. This happened to me about once every generation! It was rather annoying too, just to give you a heads up.
I played a 1000-turn Roman campaign as you can see in the stickied "post your pictures" thread. Check it out if you'd like, perhaps it could give you some ideas about expansion.