My sympathies on the class 1 - whilst I'm primarily an Engineer, I'd hate to hit something like that which impacted upon my flying. Although, as has been said, it's worth looking at the FAA licence (although it's little use for working in the UK).
Anyhow... The difference between an MEng and an MSc...
On a superficial level, you have two degrees rather than one.
On a deeper level: the difference between a BEng and an MEng is only limited extra technical content, most of the extra content is teamworking and management. That is no bad thing, particularly for people who want to go into management and generally MEng students are pretty good.
However, what an MSc offers is the potential (if you pick the right course) to specialise in something that particularly relates to the field you want to work in - and to learn that from the best people in the world in much smaller classes than most undergraduate courses. Also most MSc courses include a lengthy individual dissertation, at a much higher level than the BEng dissertation, which provides a good case to showcase your ability to function as an independent professional Engineer -that's no bad thing, used well.
That said, they're both good options - what you need to work out is the option that suits your long term career hopes best. For example, if your real passion is flying (which I can certainly relate to) then a flight mechanics related MSc such as Cranfield's Flight Dynamics offers a much improved potential to move into flight testing, similarly there are some excellent aircraft design courses, and so on.
G