“If the run would still work even without the joker why can’t you just take it??”
You can
however it seems there are a different ways to play (note how there are 4 different responses above)
The rules my set have have it my way but online there are a variety of rules most of which say it has to be replaced.
It seems in tournament games (presumably this is the most “official” way when part of a run it cant be replaced and when part of a group it must be replaced by the two mising colors (note how this is a 5th set of rules)
(Eg if group is red 8 black 8 and joker for the joker to be removed it must be replaced by yelow AND blue 8’s)