Personally I believe that there should be a choice. If someone wants to rest after every single battle let him and don't punish him. It's his choice. Yes you could say that it's also his choice to face the consequences of resting and so on but really wouldn't it be logical to chose the option that gives the most choices?
If you make resting have no consequences the newer player who is probably having Project Eternity as his first game of it's kind would allow him to adjust more easily while letting the more experience player to only rest in places where he considers it makes sense to be allowed to rest (a inn, a small room in a dungeon which you barricaded or where you left a sentry at the door). In the end both players have fun in their style of play. The newer player has more wiggling room, is forgiven for his mistakes while the veteran player still enjoys the game the way he likes it.
While having consequences would force the new players to learn and improve it could also make some of them not enjoy the game as much.
In the end I believe that the best method would be to allow you to somewhat customize your difficulty. For example when you start a new game have a menu where you choose some options regarding the game. When it comes to resting you could chose to have no consequences, have consequences ( random encounters, timers running out, bandit chief you're chasing escape), be allowed to rest anywhere, be allowed to rest in specific designated "save zones" a limited number of times and so on.
This would make everyone happy and it shouldn't be that hard to implement in the game.