I'm in this boat too....my company builds a SAAS application for marketers who in turn sell the product to their clients. Needless to say, the multiple depths can get pretty crazy in a hurry when you're trying to distribute customized info such as analytics. Here's how we clobbered the problem:
Like you, analytics hosted on the server were eating processor time alive. So, we --did-- do Google Analytics...it was just easiest for us and meant that we could leave the server processes for running our application, which is already working the server pretty hard....and it didn't hurt that it was free. To tackle the problem of access, we put (most) everything under one main account, then use the API to call data into the application based on the GA specific information for that site. Sure, there's a little bit of setup involved, but the result is good quality reporting that truly LOOKS custom, which we can then turn around and market as a custom feature.
Here's the concept pulled off in an online tut: http://freshwebtrends.com/show-off-your-google-analytics-on-your-site/13/ In our case, we used HighCharts (http://www.highcharts.com/) for charting because it's faster and better than flash, and styled the page with Jquery UI tabs as well as Datatables (http://datatables.net/) grid-sorters. All our data is pulled via direct API call to Google.
On a separate note, we do take advantage of Adobe Air reporting for our most valued and largest clients. It's a GREAT interface and allows them to quickly jump around very easy to read reports from a desktop icon. Here's a link: http://www.makeuseof.com/tag/view-your-google-analytics-account-using-adobe-air/
Obviously, there are many options out there to consider. This one just happened to work the best for my company.