I liked Beton Brut's suggestion, but to my mind the optimal solution would be a big red triangle on a white field, with no text at all. Like modern art and everything after, it allows the observer to impose their own meaning onto it:
If you like the Citgo sign because it's a landmark and icon on the landscape, you get to pretty much keep it. You can't read the letters from sufficiently far away anyway, and it does nothing to change your ability to use it as a reference point for navigation or a photo opportunity.
If you like the Citgo sign because its meaning in Boston transcends the brand it represents, or if you think the moral valence of Citgo is open to debate, you still get an iconic sign while appeasing the people for whom the debate is settled. (But deep down you get to "know" it's still the Citgo sign.)
If you hate Citgo but are willing to concede that not everyone is prepared to agree with you, you get the sign, and you get to know that Boston will no longer be associated with Caracas.
If you are a fan of modern art, you will be delighted to see the erection of a sign that acts both as a kind of citywide inside joke, and a meaningful entry into the discourse of what we do with problematic symbols.
If you are an outsider to the city of Boston, you will enjoy learning about the history of the big red triangle locals are up in arms about. Is it a religious symbol? Is it a road sign? A weather beacon?
If you want to see the sign torn down altogether, you're no fun.