At this price, the old C100 will sit on shelves for a while. I could get a a7s + Shogun for $4500. 4K, FF, ProRes vs. HD, crop, AVCHD.
With the A7S you'd also have to purchase the XLR adaptor, EF Lens adaptor, Variable ND filter(s), and SSDs which will put you closer to $6000. If your clients are asking for 4K then the A7S with shogun is a good deal and will produce an amazing image. But when doing Run 'N Gun, weddings, or events the C100 is probably a better bet since many people can use it right out of the box. Also, the Dual Pixel AF is extremely helpful for any of the situations listed above. It's really just a matter of what your needs are, what your clients' needs are, and what your budget is.
I disagree on a few things.
1. EF lens adaptor: not so much a disagreement, more like Metabones is very cheap (in this field anyway) so it's not going to upset me budget
2. SSDs have come down in price enough to make them viable, and I hardly ever consider storage device as part of the cost
3. NDs: also extremely cheap and do not remotely affect the total cost
4. XLR adaptor: I don't speak for everyone obviously, but for my work we have an audio guy so on-camera-sound is not part of the equation
So in the end, it's just the SSD pushing the cost higher. $900 for SSDs (if Metabones Canon EF to Sony E = $650)?
C100 battery: $150. a7s battery: $40 for 2. I don't mean to be difficult, but I don't see how a C100 system will save me a lot of money. Especially considering it's the OLD C100 we're talking about here. To me, I could pay a bit more to have 4K AND ProRes AND FF.
A minor note on the run-n-gun thing: I agree that for those hectic moments, the dual pixel AF is handy. But for more documentary or film (staged) work, that function is completely useless. As you said, it depends on what the needs are. For news coverage I can see how the C100 would have an advantage in focus.