I did a damage analysis between a Holy Gun 19 / Mysterious Stranger 1 and a Paladin 20 with a gun in my blog, Everyman Gaming.
If you really wanted to examine the holy gun archetype you should have compared the archetype either on its own or in the same build, either:
Holy gun 19 / Stranger 1
Paladin 19 / Stranger 1
Holy Gun 20
Both of those will show that holy gun is even worse than what your comparison showed.
Also, a typical paladin's smite persists from one turn to the other, it doesn't end at the end of turn as you seem to imply when you claim that a paladin will only get one hit from his smite levels 1 - 5. You also didn't charge the paladin the feat cost to become proficient with a gun (or, if the paladin is archer, take the whole touch AC into account.)