I work for PagerDuty. What issues are you having with the Pingdom integration? I'm sure some of our other integrations may be of interest: http://www.pagerduty.com/partners/. If you have any questions or need any help feel free to contact me.
re: using the API, we'd rather it did so also, but for the longest time Pingdom only sent out e-mail and didn't have any sort of webhook. They apparently have webhook support in their new Beep Manager offering, but that's still in beta.
re: misconfiguration, which check box are you referring to? The only two there are for ack timeouts and auto resolution.