You answered your own question
Calculating collisions with the body of your character with the guides will be the way to go, provided your guide hairs aren't too heavy and you make an efficient, lower resolution version of your characters body to collide with. Try to make this geo as efficient as possible, for example, any areas where the character has no fur delete that area from your collision geo. Separating out the main areas to sim will also help to keep your sim times down and thus make art direction decisions quicker and also it will lessen the danger of crashing. For example simming the head, body, tail guide collisions separate etc.
Another measure you could take is to make your guide hairs less flexible at the base than they are at the tip (as they would be in real life), this will help minimize the amount of contact with the body and so less penetrations…
Being able to dial in and out the result of your sim will help, for example if the fur is penetrating only a small amount, dial back the effect of the sim 10% and the penetration may disappear (this will again also allow you to art direct fur movement somewhat without the need to re-sim).
I was recently on a big fur film and all these measures were used to keep fur sims manageable. How to achieve these specific things in Houdini however is another matter, as this was all done in prop. software…