I think there's no one-size-fits-all approach. In this case, it does seem like the people who were stealing the supplies (if anyone was) got away with it, and then everyone got punished by having to do more work to get their supplies (not to mention the office manager who was fired). That's not good for morale. Also, when a system changes, I think employees who live through the change have a hard time not comparing it to the way it was before--someone who came in after the change might not have found it to be a big deal, but when you used to be able to walk into a room and grab a box of pens, and now you have to fill out a form and wait a day for the pens to arrive (and hope they are the right thing or deal with sending it back, etc.), that could seem like a huge inconvenience.
Where I work, we're going through a long, slow transition that's frustrating because it's not really transparent or consistent. Previously, we ordered all the supplies we needed directly from our office (I did a lot of it myself), using the grants my boss had brought in for our research. Over the last couple years, we've started getting pushback from the Admin Office, who has to approve each purchase--they are getting pressure from up above, who are getting pressure from external auditors, who say that we shouldn't be putting certain things on our grants, the Admin Office should be paying for them. Especially "office supplies" like pens and paper (as opposed to chemicals).
So we'll try to order something, and the Admin Office will reject it (sometimes without telling us!), and they'll say they have the same thing on hand that they can give us. Only usually it's not the same thing--it's "printer paper" but it's not the kind of printer paper my boss prefers. Also, the Admin Office is in a different building, so if they order something for us special, sometimes they accidentally have it delivered to them instead of us, and then someone from our group has to go over and get it--which could involve a couple of people and a cart if we're talking a big box of paper. You just always feel like someone is looking over your shoulder and judging you more. And while there are reasons for that (bad apples who spoiled it for others), and it's certainly a good idea to have some oversight, sometimes it kind of makes you feel like you're being greedy or a criminal when you ordered that stuff for years and no one cared.