If you’re talking about the 7812 and 7912, they’re regulators, not transistors (there’s in the order of 20 transistors in each of them), and yes they have to be in the right spot as you’ve noticed 
(the 78xx deals with positive voltages, the 79xx with negative).
When removing components, there’s usually a tradeoff: is the PCB more valuable to you than the components? If that’s the case, consider sacrificing the components – cut off the leads close to the PCB, and then clean up one hole at a time, using e.g. a toothpick to push pin & solder out.