There is nothing wrong with upgrading to a h/o alt, but unless you are dropping a 1 volt or more when you subs hit, you won't need it. Although it is sometimes considered a bandaid (in your case it is not) I would reccomend a 1 farad capacitor, and at least a yellowtop battery. If you are constantly deep cyling the stock battery (dropping more than 1/2 volt every time subs hit) it will swell up like a baloon and is really bad for it.
Yellowtop batteries are a good starting point, and are quite inexpensive.
-steven-