So, you were disqualified because you had two accounts, not because of EA.
Also, unless your EA leaves some comments for orders or has very easily recognizable pattern of transactions, broker won't know you are using EA. For the server, orders from EA look exactly like manual orders, unless of course your EA does things that are humanly impossible, like very fast or large-scale transactions.
Why people consider EA cheating is beyond my understanding. EA is *only* formalization of trading system in a form of programming language. If your 'manual' system is purely rational and not based on hunches or instinct that you can't explain, it is not different from EA.