Clerics and Druids both cast divine spells. Why is it not a problem that they both get their powers from their gods, while it apparently is a problem that Monks and Psions get theirs from mental discipline and special training?
Mostly because divine spells are mechanically similar to other divine spells, they stack with all other spells in regards to multi-classing, and (if you pick the right god) you can get the spells from the same source.
Ki is mechanically different than Psi. Psi does not stack with Ki for the purposes of multiclass. Psi doesn't even stack with magic in general save for a few line item exceptions.
Story-wise, Ki is a different branch of magic than The Weave, and is specifically "the element that flows through living bodies." Conversely Psi is explicitly not magic, comes as a reaction to the far realms, and is specifically "a source of power that originates from within a creature’s mind." Which seems to imply that Ki is tapping into some sort of all encompassing force, like a power grid. And Psi is the opposite of that, being the origin of the power and broadcasting it in a directed fashion.
Another way to say it is that Ki, and all magic by extension, is a natural part of the universe which can be manipulated by an individual part of the universe. Where as Psi, and all psionics, is displacing or over-riding the established universe and replacing it with your own.
The major confusion from all of this, is the implication that Ki and Psi are utilized in a similar manner, despite coming from different places. Sorcerers are another sore spot, in that their magic is supposed to be a part of their being (also, they use points to augment their magic, which again do not stack with Ki or Psi). But the Sorcerer's theme tends to be on the side of genetic lineages, or some other collective origin that is greater than the "self."
It can seem like splitting hairs with all these power sources, methodologies, and origins. Personally, I had to imagine all those connections as an electronic schematic for it to make sense to me.