Yes, I can't believe they have to survive on 1000 euro/month in Brussels. I thought that some unemployed already got 500 euro of social security (which is already too little to pay for food and accommodation).
There should definitely be a uniformation of the salaries, but 6000 euro is probably enough. Belgian MP's get just a bit under that anyway, and it is probably adapted to the cost of life in Brussels. So paying the EU MP's just a bit more (even 7000 so as to equal the British and German salaries) would be just fine, IMO.