It sounds like you guys are going through some ups and downs as far as making progress is concerned. Try to keep in mind the good things that she does (e.g. holding your hand in bed), and give her verbal appreciation for stuff like that, even if it is hard to do when you are thinking about the times when she slipped up.
There's no need to excuse her out of her bad behavior, but be as sympathetic as you can about the NRE. It really is hard to keep things in perspective when you're in that NRE fog. She's going to make some decisions that aren't very smart. You can help with that by stepping up the number of verbal reminders, and she may need a wake-up call now and then. But you'll have to walk a fine line here, as you don't want to ruin the marriage (or throw it away) if you can help it.
Try to keep the communication process going as a negotiation, and try to give the marriage counselling some more opportunity to help out. I think you and your wife are both in a fragile headspace right now, in your respective ways. The decisions you make today could have an enormous effect on the direction of the future, so make all those decisions with care.
Love means never having to say, "Put down that meat cleaver!"