I don't think Eb is necessarily the bad guy BUT I do believe that he's willing to perform heinous acts in a twisted attempt to save Harry.
Why? Well Harry has gone down the same path as his mother Margaret LeFay and got mixed up with some shady folks:
Margaret:Raith, Lea and Adriana.
Harry: Mab, White court, Red court, Denarians, Hades, etc.
I think that Eb told the truth about separating himself from his loved ones (Margaret) and as a result she died.
He then refused to claim Harry UNTIL the boy was about to be executed. At which point, Eb stepped up and trained Harry in isolation with a specific moral compass. This resulted in Harry becoming a private eye who wanted to help folks.
However, Eb kept the family connection a secret from Harry...maybe to protect himself or Harry.
Now Eb sees Harry's connection with the most powerful and potentially dangerous characters in Dresdenville. Also, the wizards are whispering amongst themselves and Harry is both powerful and obstinate as hell. Oh no.
So Eb, being the Blackstaff, is deploying every skill and tactic available to SAVE HARRY! I will not be surprised if the following is revealed:
1. Eb mind-screwed Carlos to track Harry & add him to security detail.
2. Eb magicked his way into Svaltalves compound to get eyes on Harry then later set it on fire to allow Thomas an opportunity to kill Etri.
3. Eb mind-jacked Thomas to kill. (#2/#3 effectively removes Harry's and Maggie's home-base and forces Harry to find a safe-haven from Maggie).
4. Eb has mind-jacked Harry (or his a tracker on him) which is how he keeps finding Harry in the damndest of places: Outside Justines apartment, on a dock in a marina.
5. I think Eb summoned the cornerhounds because...we only saw them the one time, with Eb. He also conveniently drops the "You're a Starborn, Harry" info. Probably designed for Harry to seek his mentor for answers.
So I don't think Eb is necessarily the bad guy but I do think he has some deep/twisted shame from his past (Lefay? Wife? Work?) and is hellbent on saving Harry at any and all cost.
Side note: did anyone notice his deep rage upon finding out that Thomas is his Wampire grandson? I'm starting to wonder if Lefay herself is a product of Ebs wife and another Wampire. Maybe the HUNGER killed Mrs. Eb during her pregnancy.
---Could create another parallel...Harry had a kid with a pseudo-Rampire. Hmmmmm...