Thanks so much for your votes and comments on this issue.
JIRA Service Desk 2.5 has been released with the ability to customize the Help Center and we all hope you take it for a spin! JIRA Service Desk 2.5 contains lots of other goodness and you can read the full release notes here.
After analysis of this issue we decided to move forward favoring ease of use by building an editor for the help center. The ability to add custom html/css is not something we can put on our short to mid term roadmap. Therefore we think it is only fair to not keep this issue as open and close it as "won't fix".
We have also created two separate tickets to keep tracks of your other customization needs. Please vote on the suggestion you'd like to see first:
Help Center Footer Customization
Help Center Body Customization
JIRA Service Desk Product Management