The current request is for Apple to build a special version of their OS which can be loaded onto the suspect's phone. It seems to me that the precent this would create would be for similar actions: providing custom software. The gulf between that and altering the public builds of iOS is vast, and I don't see how the former precent could possibly lead to the latter. In fact, the order in question explicitly states that the software provided by Apple must be tied to the specific iPhone the FBI wants to crack.
The precent of providing custom software for a specific device could very well be dangerous in and of itself. This comment does a good job of discussing the possibilities there:
https://news.ycombinator.com/item?id=11120036
In short, the precent set here could very well lead to requiring Apple to turn on suspects' microphones remotely, or loading software that scrapes data as the user uses it. That could certainly be bad. But it's a huge leap from that to somehow preventing Apple from ever building and selling secure systems.
Edit: thinking about this a bit more, here's what I see as the really simple version of it all. The FBI's order is compelling Apple to build something, and the worry is that it sets a precedent for building more. But forcing Apple to build insecure devices in the future is not the same; that would be preventing Apple from building secure software and hardware, not compelling them to build something insecure.