I agree. Do away with CPU mining altogether in CGMiner. You'd be doing people a favor by not letting them waste electricity on an unprofitable venture.
True, if you're mining with GPU's and augmenting with CPU, it will decrease your profitability, but if you're mining with CPU's only, it will be at a loss. Even with very conservative electric prices, take for instance an Intel Core i7 950 @ 130W producing 18 MH/s, enter those numbers in the BitcoinX Profitability Calculator with an electric rate of 0.08 and exchange rate of 7.5 (I'm using EUR instead of USD in this example), you would be losing about 5.50 EUR per month on electricity costs (and mind you that this example is a "social rate", it is the very cheapest electric rate available). CPU mining is at this point (marginally) profitable only for those who don't pay for the electricity it uses (that is, those who use others' resources - it would have been more efficient to just outright steal real money directly from them).
If stripping it out improves portability of the code, then why not? Though it is a shame of all the work that went into it. But at the very least it would prevent malicious 'users' from embedding it in their malware and getting cgminer taken up into anti-virus definitions, just look at what happened to Ufasoft's SSE2 miner.