Hi Juliette Alpha,
After reading your post, it's a realistic estimation that it's going to be the best part of 3 years before you start applying for the mentioned Cadet schemes (If there still going), or Flight Training Organizations. With that in mind, I wouldn't take any notice really with what you previous gliding instructor said. When I first undertook a few hours flying, exactly the same thing was said to me. The instruments are right in front of you and it's going to be integration for any student who has been using flight simulation beforehand and is now learning the basics of Visual Flight Rules.
Flight Simulation will certainly help you in terms of some stages of PILAPT testing which is required by most FTO's before enrolling on an Integrated course, said Cadet-ships undoubtedly. This is because PILAPT testing uses a joystick to test the candidates ability to keep the cross-hair central, while throwing in some force-feedback and alike.
Personally, I cannot see Flight Simulation whilst sat at your computer desk benefiting you a great deal in terms of the actual 'flying', however when you come on to Instrument Flight Rules (IFR), you could certainly use it to your advantage and practice procedures such as ILS approaches, Flying a VOR..etc.
Everyone will have a bad habit upon starting to Fly, very much the same as starting to Drive, but I honestly cannot see Flight Simulation at home contributing to that.
I hope that helps.
Regards