Sorry for the negativity, man. I hope this thing succeeds in a big way. Only consider this point a little while, and don't rule out grepping through the code base with the name change just now.
The meaning of words changes all the time. I don't think this is a big issue. If Code Shelter does good work and establishes a positive reputation, the phrase will generally develop positive meaning.
The degree to which the word shelter has negative associations for some people is not something I would see as deal breaker territory.
I will add that there are far more uses for shelter than just homeless shelter or animal shelter. Just a few examples:
A book about a New York woman's house hunt was titled "Gimme Shelter." (Author: Mary Elizabeth Williams)
The basic essentials in life are typically listed as food, shelter and clothing.
Shelter from the storm is a well known positive expression for sanctuary during a crisis.
Shelter magazines is the umbrella term for magazines having anything to do with homes, such as home plans, bed and bath, kitchen makeovers etc.
I think the order and placement of the words is also important.
The format "(noun) shelter" is similar to and might more readily bring to mind "animal shelter" and "homeless shelter" than a phrase in the "(verb) shelter" and "shelter _____" formats.
Personally, I liked the name and logo. I do see the points about it being taken negatively, but I didn't take it that way, and I had a reasonable guess at what the project was after reading the first two words of the headline. Just one data point.
