Looking at the cleric as a bundle of resources for a moment:
Both wells and clerics generate water. A well accesses underground aquifers* and can generate larger and smaller volumes of water depending on local circumstances. Furthermore, most liquid intended for human consumption is vaguely alcoholic as a purifying measure.
A human will consume 3-4 liters of potable water per day, and some more in other activities. A cleric, therefore, can't make all that much water relative to a village's needs in a day where 0th level spells are restricted. Therefore, from a practical matter, it's much easier for the cleric to cast "purify food and drink" on the well or on a local drawn reservoir than to create water.
However, this is not the interesting case. The interesting case comes from economies of scale and opportunity costs.
Treating a cleric as a well means that for every "well-like interaction" the cleric cannot be doing other things. Therefore, if a cleric did serve as the village's water source (cleric-as-well) they would start the day by filling a container with water and then go about their normal business.
Therefore, if you want a poisoned well scenario here, you must poison the cleric.
From a more practical matter, this one interaction costs a minute or two of time and doesn't place much stress on the cleric. It does, however, increase the villages' dependence on the cleric and reduces the overall food supply of the village (see purify food and drink, which is a "I can't believe this wasn't stored in a fridge" spell that does enormous amounts to increase food efficiency by preventing spoilage. Thus, it's the cleric's best interest to see that the well is purified since more people will benefit.
There is also a single point of failure here, given that the cleric quite literally has the capability to deny life to anyone in the village by simply choosing her spell choices differently. The villagers may not like to be so dependent on the caster.
Creating an economy in a 3.5 world is interesting, depending on the social constructions you have available. I recommend reading the various tomes here by K as to why Feudalism. Considering that the new world expedition was funded just to have easier access to pepper, entire plots can hinge around finding likely students who can learn to cast purify food and drink. Poisoning the well could be literal (causing starvation) or figurative (magical well of energy that powers divine links, etc...) or political (a new cleric's in town, and she says that casting these spells defiles the miracles granted by the gods.
Given that this is not a post-scarcity society, resource deprivation is always possible. It's just may attack different links in the network.
For an interesting thought experiment, consider the destablizing potential over a hundred years of a wondrous item of fabricate, a wall of fire made perminant, and a wall of iron spell.
"The difference is that in Pathfinder Cantrips and Orisons are effectively "At Will". This means you can create water till the cows come home."
Then you get into the relative utility of time and economies of scale. Every round spent producing water is a round that isn't being used to, for example, purify food and drink. (I hope I made that point clearly enough in my answer) In the grand scheme of things, one cleric preserving a village's food supplies across winter means a whole lot more accessible food from their environment. Probably far more than the consequences of refrigeration. Farming patterns shift to high-calorie crops instead of preservable crops, and villagers can start achieving remarkable efficiencies.
For one thing, the average calorie intake of each villager goes up tremendously. Which produces healthier villagers who are more able to meet their adventuring capacities, which produces more clerics. This sounds like a virtuous cycle that will quickly strip the lands of reasons for Feudalism, which means that some counter-force is required to remain "expected authenticity." Don't even get me started on the consequences of rings of sustenance on a village's production capacity.
* Aquifers do not generate happy thoughts in dwarves.