There are some things about this that I'd like to know more about:
1. WHY do they want the photos taken down? Does the email specify that? If not, have you asked? Something else the OP said suggested these are largely photos of other employees, and so--as another poster mentioned--perhaps this whole thing is because someone saw a photo of themselves and didn't like it being online? Or perhaps the company simply fears this MIGHT happen.
2. WHY does the OP want to post the pictures personally? Are you aiming to make these a part of your professional portfolio? Are you using them to solicit other photography business? According to your sig, you have a D5100 and a 50mm prime. Not exactly the stuff professionals carry (not knocking the OP or the equipment here--I have the D5100 as well--but it's NOT pro equipment). WHAT is the benefit to the OP of being able to post these photos?? In other words, is this really even worth all your anxiety and stress about it, or would it be better to just let it go?
I do 99% of the photography for my employer, including photos of press conferences, award ceremonies, etc that sometimes get published (in goofy little local media outlets or our horrible daily newspaper, not in anything impressive!). They also get put on our website, FB page, blog, etc (by me, since I'm also the Social Media Guru). However, like you, photography is not part of my job description, unless you lump it in that pesky little "other duties as assigned" phrase.
Regardless of the answers to those questions, two things seem obvious to me (assuming you like your job and plan to stay there):
1. You are very likely S.O.O.L. (Sh*t Out of Luck) for this particular incident. Live and learn.
2. You need to get this worked out so that both you and the company understand who can do what with your photos.
Otherwise, you'll end up in a situation like I found myself in recently. I took some photos of a company event a few years ago, and they discovered I actually had some skills (more than any of them!) so I become the "unofficial official" photographer, although it is NOT in my job description (except under that pesky, "and other duties as assigned" catchphrase!). That was fine, and even the occasional photo of mine that got printed elsewhere without credit was okay, since I knew that they weren't really award-winning photos anyway. But then one day, I came across two of my photos, published in a fairly large-distribution trade magazine--one was a full-page photo. This time, credit WAS given--to someone ELSE!! THAT hurt my pride!
I am now in the process of drafting a written set of "guidelines" for the use and rights of any photos I take for the company using my own camera equipment, so that they can use what they want, when they want, but the photos are still MINE, and credit has to be given, and I have to be made aware of anyone outside the company being given permission to use one of my photos.