Looking at it again, you are right... that list sucked. I do however think that Guild holdings have a case for being better at espionage, since where there's exchanged money, there is also exchanged money below the table. So to speak. However, it's not an overly compelling case, no.
Putting that aside...
To a certain degree, manor and guilds already have a niche. Manors can raise levies, Guilds can affect Trade holdings. Manors role is not that strong though, since levies are something you usually only use when the shit is about to vaporize the fan, but then they are very useful. Temple have a niche in being necessary for realm spells, same as sources.
So far I only see one solution, to the problems mentioned by Bjørn. It is to use the list Bjørn laid out and then remove hardness from the board. Holdings only help you do things, not defend against them, unless it is the holding that is being directly attacked. Inderectly holdings would still help you defend, as e.g. Law has a lot to do with prosperity and prosperity is, among others, the "armour" for your holdings. Perhaps more directly, your holdings provide income that help you defend yourselves through influence, and they give you the ability to spend influence.