In my experience, civilians working within the military organization can be a challenge, or an asset. In CA, we have both dual-status and Title 5 (non-dual status) Federal Technicians, and while I don’t currently lead any, I have in the past, and have also been one. Like @fightingengineer said, you have to tread lightly when leading civilians.
One of the biggest eye openers to having civilians within the organization was that they are unionized; which can mean it’s almost impossible to fire them.  In one instance, an M-Day/TPU “Soldier” was separated for repeated failures of the APFT and Body Comp. She was a dual-status technician, which means she lost her tech job. Oh, but wait, there’s more. The union got involved, and then got her separation revoked.
Civilians can have a negative effect on discipline, many adhering to the strict letter of their position description. When I was a GS, I got counseled because I chose to eat lunch at my desk so I could knock out emails and work; I was told this makes the “the other techs look bad.” Something working with civilians a leader has to understand is that many civilians will work hard, right up until their 15 minute break, lunch, or quitting time. Then good luck. Yes, as a Soldier this seems like “whaaaaat?!?!” However thanks to those same laws, rules and regulations that dictate what a civilian can do, can also get said civilian, or you their supervisor, in trouble if you try to squeeze a “free” couple of minutes out of them. A civilian must be compensated for the time they work. Bottom line.
Another negative I have seen in many civilians (as well as Soldiers in some personnel sections) is they forget who they work for. They work for Soldier, Commander, in short, me. The range tech who acts like they are doing you a favor for running the pop-ups for your qual range, you know, their job. Or the CIF tech; “seriously dude?!? It’s dirty!!! It’s still in the original wrapping!” How about the personnel tech who takes their sweet time processing personnel actions?
That’s not to say they are all bad. Civilians are also a huge source of institutional knowledge. Green suiters rotate out, but the civilians can be there for years, doing the same thing, learning the tips, tricks, and insider skills that can only be developed over years of doing the same job.
I guess these are just some of my experiences that have jaded my perception of civilians in the military organization structure, which is not to say most are bad. As many here have said, the biggest thing is to bring them into the fold and not treat them as “other.”