Yes, I've been running 3s exclusively, but I won't say that's a "problem." I've been running an average of 1 3200mah pack through it a day (some days I've run 3-4 packs, others not at all) since I got the truck 6 weeks or so ago, so similar run time to what you've had. Yesterday was my first outing with the 7200mah pack, I haven't charged it to see exactly how much I used, but I'd imagine I ran a bit over 5000mah before I heard the crunching.
I'm not at all complaining about it, if I wanted it to never break, I could always switch to NiMh, or buy a Slash! This truck has been reasonably reliable, power and usage considered. Just like with our crawlers, if something breaks, we want to upgrade so that we can continue driving it in the same manner but more reliably.
I switched to the 10T pinion after the first couple packs (truck was WAY too fast for the space I have available) so it definitely has much more punch off the bottom, which certainly contributes to the diff housings deforming. I'd rather pay for an aluminum housing than cut the power back.