Harsher in Hindsight: At the time, the concept of Regeneration really wasn't as fleshed out as it is now. At the time, the Time Lords were just making the Doctor 'change his appearance' in preparation for his exile. Now, it's more or less the Time Lords killing the Doctor (in the sense of forcing him to use one of his 12 regenerations) before they exile him, in essence this was a summary execution.
Likewise, Jamie and Zoe's fates (being mindwiped and sent back to their own time with no memory of their adventures or one another) seemed to have left a lasting scar on The Doctor, causing him to be a lot more distant to his Companions for a long time to come. But come 40-something years later and "Journey's End" where he has to be the one carrying out that fate to a Companion, despite her begging him not to? Ouch!