The Romans and their automatic protectorate canceling is related to a hardcoded feature which applies to all AI controlled Roman factions - they automatically declare war upon whoever their Roman allies are at war with on the turn after war is declared, regardless of previous stances or agreements made. If a Roman faction agrees to a ceasefire/protectorate with another faction, and other Romans are still at war with it, the ceasefire/protectorate will automatically conclude the following turn.
The senate is, however, the item that is holding this system together. Destroying them gives all Roman factions full independent diplomatic status, which also can result in an early civil war.
If the senate isn't destroyed, however, there is a way out, but it's tricky. The faction has to offer every Roman faction (including the S.P.Q.R) a protectorate/other war canceling deal on the same turn, and every faction has to accept. This is nigh impossible, so you'll probably never gain a protectorate with any Roman faction at any point while the senate still lives on.
Gah! Telys sort of beat me to it. My fingers are aging too quickly!
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