Legions were supposed to disarm (edit: disband) themselves before coming back to Rome, in order to discourage any coups.
As far as I know, legions weren't required to disarm or disband when returning to Rome, which makes sense: you didn't want the army to be unable to defend the capital if the Gauls or rival generals attacked the capital.
The rule relating to Caesar crossing the Rubicon was that Caesar had been granted proconsular authority only over Cisalpine Gaul and Illyricum (and later over Transalpine Gaul as well). This meant that he had no "power of command" (imperium) outside of those provinces -- it would have been just as illegal for him to lead an army into Spain or Greece as it would to lead it into Italy. Technically, he lost imperium when he crossed the border, i.e. his soldiers were under no obligation to follow him over the border and he had no authority over them. However, Legio XIII Gemina (like just about every legion Caesar commanded) were fiercely loyal to him, and continued following his orders even though it was against the law. To clarify: my understanding is that the law didn't say that legions were automatically disbanded when they crossed into Italy, but that it was illegal for a general with imperium to lead the army somewhere where he didn't have imperium.
So who could lead an army in Italy? Anyone given that authority by the senate. This was generally the consuls, the highest elected officials in Rome. When Julius Caesar crossed the Rubicon, these were Gaius Claudius Marcellus Maior and Lucius Cornelius Lentulus Crus. With Caesar's approach, however, effective control was given to Pompey, who was already under orders from the senate to raise 130,000 soldiers to defend Rome from Caesar. Note that these soldiers were in Italy at the time, armed and ready to fight -- so clearly leading an army in Italy wasn't itself illegal! Pompey opted to retreat to Greece with the soldiers under his command, where his allies could provide troops and supplies to him and his army. The rest, of course, is history.
I couldn't find a lot of information on the no-armies-in-Italy rule, so hopefully someone else will contribute some here. There was definitely a no-armies-in-(central)-Rome prohibition, based on the Pomerium. This law was important enough that most of Sulla's commanders refused to violate it in 88-87 BC. Incidentally, all of this is based on pre-Imperial Roman history -- in 28 BC, the Caesar Augustus was granted imperium over every single province, so he (and all future emperors) outranked every general, magistrate, governor, proconsul or consul anywhere in the empire.
To answer the rest of your question, I don't think Roman legions were often deliberately disbanded: there's records of legions mobilized over several hundred years, which I assume means that soldiers would be honorably discharged after serving for a standard 25 year term -- and, if they weren't Roman citizens, be granted citizenship for their service. I know there are some records of legions being disbanded, either because they could no longer be trusted, such as Legio IV Macedonica (in which case a "new" legion with the same number was immediately raied) or after a particularly brutal loss, such as Legio XVII, which was lost in the Battle of the Teutoburg Forest and whose number would never be re-raised. but I don't think Roman legions would be uniformly disbanded at a particular place or time.