It's not without precedence. Look at what happened to the IT contractors, with the IR35 legislation.
The government line was that they were avoiding paying the right amount of tax and I would see this initiative as being similar, "aircraft owners are avoiding European harmonization."
If you operate an aircraft off the G-reg, you have to accept the risk that government action may close your options. It's the same with most areas, where individuals seek (quite legally) to work around legislation. When that legislation is altered to close the loophole, perhaps you have to accept that times have changed and reassess your position.