Consider making your merchant script more 'smart'! Despite the inability (and sometimes intention) of customers to send proper payments, you should think of how much is missing (total percentage) and is it worth the hassle with the delayed and pending order.
Compare it e.g. to bastards from hell PayPal. They deduct a noticeable percentage as fee. If the percentage you miss is below that, don't care and swallow it. At least with Bitcoins noone can freeze your account or charge back the payment. That alone is worth it over fu***** PayPal.
Nothing wrong with Paypal. They may deduct fees but they do accurately inform your script that payment arrived in full and allow script to trigger.
But BTC-e does stupid things confusing people and scripts.