When Doctor Who began in 1963, the Doctor was newly on his own, having recently turned his back on Time Lord society, forfeiting his birthright, and becoming one of several renegades. As the Eighth once explained, "half of my lot are crazy and corrupt, and the other half, well, they're duller than you could possibly imagine."
The more we saw of Gallifrey, the more viewers understood the Doctor's reasons for leaving his home and its rules. The High Council of Time Lords revised historical records to ensure they didn't look bad. The black ops Time Lord organization known as the Celestial Intervention Agency (CIA) didn't mind interfering in history and breaking the "laws of time" to ensure nothing threatened Gallifrey's power. And nearly all of the Time Lords who were in charge of things had a low opinion of the Doctor, despite his heroic nature and popularity with the lower classes (or perhaps because of that).
After the Doctor had been a fugitive for the first six years of the program, he was finally captured and put on trial for all his interference, facing a sentence of execution. All those battles, all those lives saved, and a Time Lord tribunal still thought it might be a good idea to wipe the hero from existence. The Doctor convinced them this was a bad idea, but was still forced to regenerate and live in exile on Earth for years as its protector (sort of like community service). Even after his exile was lifted, the Doctor was obligated to do the occasional mission in exchange for his continued freedom. He was put on trial twice more, each time as part of a scheme by corrupt Gallifreyan officials.
If the Time Lords do come back, they may still have their share of corrupt leaders. Even if they don't, they may not approve of how the Doctor, a barely tolerated renegade and convicted criminal, banished them to a pocket dimension and since then has let things get so bad that he's actually had to reboot the universe once or twice. Would they bother with another trial? Maybe they'd just decide to shoot him on sight.
Alan Sizzler Kistler (@SizzlerKistler) is the author of Doctor Who: A History. Paul McGann is his Doctor.