Are there any words whose spelling was deliberately changed to make them non-offensive?

Solution 1:

The seed of Guizotia abyssinica used to be known as niger seed. That combination of letters is pronounced differently from the much more common word with a similar spelling, and the difference should be obvious because of the single g. But you'll find it much more commonly listed (e.g. on packaging for bird food) as nyger or nyjer™, a phonetic spelling that dodges any confusion (perhaps not helped by spell checkers not including the original spelling).

Solution 2:

Did you know that the original name for Pac-Man was Puck-Man? You'd think it was because he looks like a hockey puck but it actually comes from the Japanese phrase 'Paku-Paku,' which means to flap one's mouth open and closed. They changed it because they thought Puck-Man would be too easy to vandalize, you know, like people could just scratch off the P and turn it into an F or whatever.

-- Scott Pilgrim vs The World

EDIT: Fact-checked: https://skeptics.stackexchange.com/questions/37847/was-pac-man-originally-named-puck-man

Solution 3:

It is not quite what you're looking for as the spelling wasn't changed just a little, but rapeseed has been changed to canola, to protect people's sensibilities about rape.

Solution 4:

Not quite what you are asking, but something similar is found in proper names. The venerable Scottish surname ‘Smellie’ is nowadays often changed to ‘Smillie’ (itself a genuine variant e.g. Wikipedia article on Robert Smillie).

However some Smellies (including my former boss) strongly resist this, as exmplified in this article in the Daily Telegraph.

Addendum

You still have to be careful with people who spell their surname Smellie. Some of them pronounce it Smillie.