Exactly…
If a guild or temple is collecting vast sums of gold and the ruler of the provinces is poor then said ruler isn’t going to sit by and let all that gold go to waste (or at least he shouldn’t). He will raise taxes and start using the extra money to fund more armies or ships and buildings for his realm.
It is true that guilds and temple do end up with a lot more money than a king, but this is not that unrealistic when you consider that the guild control most of the mercantile activing in a kingdom and the priests own land, farms, etc and are given money by the citizens. All the king has are his taxes, and you know how much people complain about them.
It is the DMs job to find something for all that nice gold the temples and guild collect to be spent on, or to find ways of taking it away from them without them realising that is what you are doing. The easiest way to do this is through conflict, either war or a battle with another major guild or temple. Nothing eats through your treasury like a war. A wealth realm is always going to the target of those who seek its wealth.
Other ideas could include a natural disaster, where the regent is forced to spend some of his wealth to help the people. How about a rebellon, something like the French revolution. No one likes to see a wealthy merchant sitting there in his palace while the poor suffer and if your regents have huge treasuries then that is going to cause some friction with the people who will start demanding a share of the wealth. If a lot of regents have huge stashes of gold then this rebellion could grow and spread across a wide region, not only upsetting the PC realms, but also NPCs. If the people fell in behind a charasmatic blooded leader and the military started deserting (they are promised a share of the plunder when the evil grasping PCs are driven from power) then you have a major problem and it could be something that carries on for turn after turn, as the PC strive to reclaim their realm from the rebels.
Corruption is also a good one to use, starting small with just a few hundred gp going missing, but soon large amounts of gold start vanishing from the treasury.
Then you can look at new things for regents to spend their money on. If a temple has a big treasury its priests might start asking for a new, grand temple to be built, one that will cost oddles of gold. And of course, then you have all the problems associated with building the great temple, labour shortage, material shortages, earthquakes, and so on.
How about giving your regents something to spend their gold on that they actually want. If they are wizards or priest and have item creation feats, then you can suck away quite a few gb that way without upsetting your players. New spells to research for wizard (although they don’t usually have gold problem). How about new assets, as someone already mentioned. There was a post on the forums recently about specially holdings, let them build some of those. Or maybe a spy network, let them set up one of these, they are always expensive to run with bribes etc.
The posibilities are endless, if I thought about it long enough I could probably come up with a hundred completely different ways to take money away from regents who have too much, enough to keep the game fresh and interesting for a long while.