I have found that PackageKit is messing with the manual updates so to avoid this the process is killed. But I whish to disable or removal this program (since I do all the updates manually), but will these options make a fault for the system?,
Taken from the freedesktop.org site:
The actual nuts-and-bolts distro tool (dnf, apt, etc) is used by PackageKit using compiled and scripted helpers. PackageKit isn't meant to replace these tools, instead providing a common set of abstractions that can be used by standard GUI and text mode package managers.
I've personally never had issues blasting this out (in fact, I do it on almost every clean install of Fedora). However, the sensible answer would be to use your system with it disabled for a while, and then uninstall completely once you're sure nothing breaks.
Link to more info on PackageKit: link
Found this in the FAQ as well:
Can users still use their normal package managers and backends, such as Yum, APT or Conary? PackageKit does not stop you using the low level tools, in fact it quits as soon as possible if a native tool is waiting to be run.