1. You are listening to people who don't know what they are talking about. Your girlfriend will not get a ban for making a valid visa application. The travel agent does not know what he is talking about. That is poppycock! She should go ahead and make her application as her grounds for doing so are strong. She is now in a relationship with you and can apply as your partner. A person who can show they are in a settled relationship for two years with a British citizen who earns more than GBP 18,600 can get a spousal visa to live and work in the UK.
2. You don't get banned for not having sufficient money to fund a trip. You don't get banned for wanting to apply and pay application fees to get into the UK on a tourist visa. Even if your girlfriend did get banned, she would get any ban overturned on appeal. The appeal procedure is to an Upper Tribunal in the first instance. You can also make a judicial review of any decision. So you and your girlfriend are worrying unduly.
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4. What I would suggest is that you pay yourself a monthly salary from the business which can be extrapolated over the full year so your earnings are above the necessary GBP 18,600. If you want you can pay yourself this amount over a four month period so that you exceed the earnings threshold in the current year. It is only done on a current year basis so once you show you earn the necessary amount that is sufficient. I appreciate that accounting within a business may show small sums being produced. However, you should simply mould your earnings stream so you exceed for the year in which you are making the application. It is your earnings which are important if you apply for the partner visa, not hers.