Well the Comixology support page there linked states in bold that IDW comics will still be available through them and the PR fluff IDW Q&A would appear to support that.
IDW previously maintained their own app anyway so it makes business sense for them to maintain a digital storefront where they get more of the pie from each purchase. They've been doing motion comics with Madefire for a while so it's logical for them to partner with them, also making their motion comics much easier to buy.
I do approve of digital comics being available from multiple vendors. Having, for example, Comixology as the only online digital vendor for comics would not be good for the industry or customers.
Indeed, just as having Diamond as the only distributor for physical comics was a poor thing for the industry having a single digital outlet would be equally unpleasant. I am pleased to see IDW maintaining their own digital option alongside their Comixology deal, having that choice available is a good thing for the market and for the consumer in my view - just as it is in the eBook marketplace.