We (my group and I) figured out, that in Pathfinder you can use True Resurrection for a price of 25,000 gp but Raise Dead works for 5,000 gp and you can remove the negative levels with Restoration (two times) for 1,000 gp. So the party can resurrect for 7,000 gp. That doesn't work if the corpse is destroyed or damaged, but in the other cases it is a much cheaper possibility. What are the disadvantages of this combination? Should I disallow that as a gamemaster?
The combination of raise dead and restoration in Pathfinder RPG is not only reasonable, it's intended.
The price difference is a holdover from D&D 3.5, where the combination of raise dead and restoration was actually much weaker than true resurrection. In D&D, raise dead caused a full level loss instead of a negative level, and restoration could not restore the lost level. As the only spell able to revive a character without level loss, true resurrection was significantly more valuable.
In Pathfinder, restoration was explicitly given the new ability to recover permanent negative levels, at the increased price at 1,000gp per level. This suggests that the designers intended for the combination to be available.
Even so, true resurrection still has advantages:
I think you've answered your own question.
As long as you have the corpse, and it is in good condition, there is no reason not to use Raise Dead.
True Resurrection is only needed when the corpse is no longer around.