I'm a little late to the thread, but as someone else that thoroughly enjoyed Heist, I have to say that I completely agree with your 3 main points.

As far as the gameplay of Heist itself, I think it would be worlds better if no reward chest ever got sealed off - not the mini chests, and not the grand heist reward. When the meter first fills, guards should just start flooding the area, but you should still be able to kill and loot as you please. The bar should just be able to fill up multiple times (past the first fill, it could fill in orange, then red, etc) and more (and more difficult) guards should spill in with each checkpoint. Obviously, the amount of alert generated would want to increase in exchange.
If they keep the loss of items on death, this just increases the tension, as well as feeding more directly into the usual PoE gameplay loop. If you can kill more things, you can get more rewards. As long as you can keep the guards off of your mercenary, he/she should be able to take their time to (hopefully more quickly than they currently do) open doors & chests.