I agree that this is a problem inherent in the D&D rule structure. It was even more of a problem in 3 and 3.5. I can see having a problem with players blowing their dailys in every encounter and then resting afterward to get them back. Here is my advice, build some encounters that are just barely dangerous. Blood sucking worms, a handfull of minions with one brute leader, a single low level slime, something like that. Make them easy encounters, lower level than the party. That means that the xp the party gets from them is neglageble. However, they still break up a rest. You don't get the benefits of an extended rest if you have to fight every 3 hours, even if it's an easy fight. Now, hit them every time they stop for an extended rest in a room that isn't safe. Space the "safe" rooms sufficiently far apart and they will have to face multiple encounters without resting if they want to progress through the dungeon.