I would think CF would be far more reliable than your average microSD card.  I work for a manufacturer of high-performance storage servers who used CF cards as boot media for many years, and data getting corrupted or cards getting worn out is extremely uncommon and usually caused by a power failure during a write.  If you really want to be sure, use an "industrial" grade CF card with SLC flash.  They aren't cheap, but have very high write endurance.  In all honesty though, a standard CF card from a reputable manufacturer is probably good enough for 99% of retro hobbyist use.

I personally suspect a lot of the Raspberry Pi's SD problems stem from cheap media.  While the Pi itself is surprisingly well made for a computer that can be bought for less than the cost of a movie ticket and popcorn (and I think the fact that it can be manufactured in Wales at a profit says something about those who claim it would be impossible to make iPhones in a first world country profitably), distributors often tend to pair it with the cheapest of the cheap SD cards, WiFi adapters, etc. to keep the price of 'kits' they sell down.