If I may turn this into an Ideas tangent, I think what this inequity reveals is that the vassal system ought to have some kind of interacting limitation with cultural pressure. As well, diplomatic options in general need to not be processed in isolation, player-to-player. Some things are isolated, like trading a good, but options like defensive pacts? Surrendering a city to one of two attackers? Declaring itself. And, vassalizing.
Brief suggestion, when civs willingly vassalize, the master should have to agree to declare on all the vassal civ's enemies. There is no logic - but bad gameplay - in reversing this to make a peace happen on the vassal. You can't just cause peace, the conqueror has a say too, obviously, and this is one of the limitations of the "isolated" diplo system.
The above requirement would have diplomatic consequences, and balances out willing capitulation.
If a civ capitulates, there's one of two possibilities: Either the master and you are at war, or you're not at war. If you're at war, then the vassal is either an enemy that became an enemy's vassal, or is a third party that has been turned against you. All straightforward. If you're not at war, this is where the mess happens.
A civ capitulating should create some form of safety and be guaranteed to do so. Causing peace is out of the question, unless there was a multi-way diplo screen possible. Let's just assume it's not, for now. (But imagine China coming up in front of Kublai and Tokugawa, and suing for peace from -her attackers plural-, in which she offers Capitulation (Kublai). But the technical work is immense.)
Peace isn't free, but anyone can declare war. So an alternate is to make the master declare on the vassals enemies as before. But this is unlikeable, because it makes anything resembling the above ideal totally impossible; you can't arrange with your conquering buddy to get the vassal to whom wants it, not without letting any one of the three players get tricked under a white flag. Peace and war are the only two things that can be used to make the master "forced" to somehow protect the vassal*, so the search is narrowed. I think the only solution within the scope of two-party diplo is to change vassalage rules subtly, so that the capitulated vassal remains at war with those civs it was at war with, while the master may choose whether or not to join at capitulation. It has the same diplo limitations, but it can obtain peace with those civs, one-by-one until there are none of them. In this proposal, you get the noxious consequence of the master civ wheeling and dealing over the bloody battlefield of its vassal, which is nonsensical itself. And a state of No Trade is just war with borders.
Which brings me to the culture interaction.
*I would like some interaction with the culture system, where, in whatever way culture or religion is acquired and pressures other civs, and which allows the vassal to otherwise liberate itself, a fine addition to vassalage would be a penalty for "default" of the vassalage arrangement , paid in the form of that same culture resource. The big question is how to measure default.
So, within the system, the only thing that -could- work is to make the master declare on the vassal's enemies at signing, capitulation or no, just as the vassal loses freedom to say otherwise from the master from then on, including conditions for peace^. I really want multi-way diplo, though.
^Last moment insight. Maybe the master declares war on the vassal's enemies, but if this in fact would declare a war, and it was capitulation, then trigger an immediate diplo screen between the master and that enemy player, where they negotiate peace between the three of them. The master is in a proposal for war with the other enemy; he must somehow obtain the offer of (No declare) which comes under a two-way Peace (You & [vassal]). If the master cannot secure this arrangement, he declares; but if he can, the other player obtains peace with the vassal and no declare happens. Works within the two-party screen, all it needs is some augmentation to let (at least) master's negotiate peace with vassals (instead of themselves) as an item.