A proto cape is a definite must for this. I purchased a bunch of pcb screw terminals to connect everything to my BB. It really makes for a clean install.
It is actually very simple to have true PID control on the BBB. There are NodeJS libraries for practically everything- GPIO control, ds18b20 reading, PID control. They all execute necessary commands with a single line of code. I used socketIO for a low-latency way of communicating between the web browser and the node server. SSR control is instantaneous and will switch as fast as you can press the button. It eliminated the need to ever refresh the page or use a more demanding method like ajax to update the data sets.
A BBB/rPi is a great tool for brewing because of the available sensors and expansibility of the system. I've implemented timers that save state if you closed your browser and working on brewing calculators. You could really fully automate everything- import a timeline of events, start the timer, and watch the system do it all. But where's the fun in that right?
Here's what I've been able to code on the UI so far. It's worked perfectly for two brews.