While Cyanogen Inc's Cyanogen OS may have other plans, the non-corporate arm of the larger Cyanogen identity, CyanogenMod, has clarified today that the community version of the ROM will not ship with Cyanogen OS's "exclusive partner apps." That means that no, your next CM nightly build will not have any Microsoft junk on it - that privilege is reserved for the exclusive pleasure of OnePlus One and Yu Yureka owners.
The distinction here is that those phones run Cyanogen OS versus the standard, community-developed CyanogenMod. While Cyanogen OS shares a code base with CyanogenMod, Cyanogen Inc can then add software or features into the builds that end up on Cyanogen OS devices, which get the Cyanogen OS name (eg Cyanogen OS 12).
In the same blog post, CyanogenMod's ciwrl provides a short primer on the new CM12.1 nightlies that are now showing up, reminding you to make sure you flash the correct Google Apps package (ie, one that works on 5.1) if you want your Google Apps to, you know, work. They also recognize a bug with the CM Gerrit for Google OAuth users who are being marked "untrusted," so if that's an issue you're having, they're working on it, and hope to have it resolved by the weekend.