K.Kinzie a nobody? Give me a chuffing break. In Saints Row IV she singlehandly escapes alien captivity herself, steals a spaceship and then rescues both the President and the Vice President. Then she helps the President/Boss get all the other Saints out of the simulation and helps the Boss get Johnny Gat back even though doing so risks them being detected by Zinyak.
The issue of Kinzie punching the Boss and why they did nothing in response has been debated time and time again by Saints fans and there is one glaringly obvious reason why they let her get away with it which is in the game's narrative itself. It's the the way the Boss treats Kinzie, as someone who they regard as so important and as a close and loyal friend who they couldn't bare to lose.
This is obviously demonstrated in several points in the game first in the White House scene when Kinzie is first abducted and the Boss yells "KINZIE NO" and runs to try and save her. Then secondly during the Kinzie Gambit when after Kinzie is recaptured by Zinyak the Boss is distressed and angry and is desperate to save her. This demonstrated palpably when just after Kinzie is kidnapped and the Boss is fending off aliens on the ship with Gat they monetarily forget Kinzie is not there and asks for her help with something (where the weakest point on the ship dragging them towards the sun is) and Gat has to remind them that Kinzie is kidnapped and can't help. the Boss gets way pissed that they forgot, and it shows how much they rely on Kinzie.
So when the Boss rescues Kinzie from the 50s nightmare and she socks them for joking about her poodle skirtt the Boss is just relieved that they have Kinzie back and let's it go. They are hardly gonna punish their most important homie just for that.