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.
