Quite a predicament. I have actually experienced a similar situation. To fully answer your questions I would need to know more about each business, such as the revenue each entity is generating, and what your role is in each. If you're profitable, and can afford to hire a replacement for yourself, and act as a consultant and/or split your time for company A, you may be able to spend more time with B. The other trouble you are describing is non alignment of partners. This is potentially a bigger problem in the long run, especially once you generate some success. If fundamentally you disagree with both, and can't align with one to vote your position, then you should probably leave B, no matter what. The stress level will only increase as time goes on, especially once real money is involved. I have been fortunate enough to have alignment with my two partners. Not to say there aren't any grey hairs from the epic battles, or that no one got hurt in the late night bun fights.

The security concerns should not be your main focus. It's getting the thing to work. I have seen countless times agencies overpromise and underdeliver. The contract needs to be structured in a way to prevent them wasting months of your time promising a product they can not deliver. The other main point to remember, is that likely you will need to hire full time, in house, developers to transition the software if you start to get traction. Most of the times agencies build code which does not scale well. Usually this is due to a tradeoff between speed of development (getting the software to you) and efficient, well architected code. My advice, whatever it's worth is if you can afford it, build it in house from the start. You will most likely end up rewriting the code once you bring in a CTO. This has happened to almost everyone I know who has worked with an agency. If you can't afford it, get as many references as you can from completed projects, structure the contract in a way to prevent garbage code, and think through your software from the start to prevent feature creep, agencies hate this, and will make your final code less efficient if you keep springing new features as the build progresses.