Take the HST's which are at the end of their front line careers. They are expensive kit, so you wouldn't want to withdraw them early, but it's probably not practical to modify most of them at this late stage. There are hundreds of them, most of which will become non-compliant at the same time. Do you think that it is practical for them all to be replaced at the same time - given that you will have to have a lot of factory capacity, involving capital investment and training, which will probably become redundant once the new fleet is built. Of course not. What is being done now - building the new fleets in sequence is the only sensible way to do this. Someone has to get their trains a bit later - it just happens to be EMT. Of course, that doesn't suit an arbitrary deadline, but then replacing trains doesn't suit arbitrary deadlines anyway.
With regard to the first part of your question, we don't tell disabled people they're not allowed to travel in a particular part of the train now, so why would we start doing this at the end of the year ?
We could paint a large red stripe along the top of carriages which aren't fully compliant. A disabled person could sit in any part of the train they choose, as now. It's just that they will have the information that a particular carriage isn't 100% compliant, and they can make their choice accordingly.