Is it possible to create an EoiP tunnel from a Mikrotik router to a Centos Linux Server? Or is there a better way to do that then EoiP?

Yes, it is possible, and there is a compileable user space daemon available.

But for the "best" solution you have possible other options, depending on your use case.
For internal use, in a secure network, you can use other simple tunelling protocols, like IPIP (if you only need IPv4 traffic) and GRE, both supported by Linux.
For external use, you can use PPTP (some claiming it being unsafe), L2TP and OpenVPN (all being also supported by Linux).
And then is also SSTP, with an available Linux implementation.
So you have plenty to choose from, unless you need pure L2 tunneling...