Are you providing PEAR packages for public distribution thru PEAR/PECL? If so then you probably want to stick to PEAR conventions.
Otherwise, I can't see it being worth the big refactor. The biggest thing is agreeing upon a coding standard for your team... doesn't have to be PEAR's standard... just make sure there is some standard convention enforced.
For instance, I'm a fan of the
function foo () {
format vs the PEAR standard..
function foo ()
{
Bottom line, don't worry too much about conforming to their standard if its going to be a ton of work, especially if you aren't putting the packages on PECL.