I think Αndré's proposed change for utils.php would be fine in 1.5.x (at least I don't see a disadvantage to that method)... but I would agree with those saying the change to include the new jquery should wait until 1.6.
While there may be no security related issues with jquery - if we were to break a theme or plugin a user relied on by including new jquery in 1.5.28, the user would be unable to apply any future security fixes (1.5.30, etc) until the jquery issue were addressed...
With 1.6, they will have the option to stay on a still supported (for a while) 1.5 version - with any new security fixes - until they can address the compatibility issues and are ready to upgrade..
I was going to suggest possibly a 'hidden' config option in 1.5.x to specify the level of jquery to include - thinking it was only used in one place (init.inc.php) - but as it is hardcoded elsewhere - may not be best choice...
The plugin using page_html hook would certainly find them all.
As a 'strategic' direction - I would think a config option in 1.6 for the jquery versions to use with all hardcoded references changed to look there might be best choice (and maybe an option to indicate include from cpg distribution or load from cdn as Phill suggested?)
Would position for users to adopt jquery 2.x before CPG 1.7...