This isn't really a programming question, it is a commercial question for your product management and marketing people. Flex requires Flash as you are aware, so the answer is to find out the degree to which Flash is supported in your customer base - and the version. Start with your biggest and highest profile customer. If you can't get away with it there it is a non-starter.
I am pretty sure that your feature set will be better as well as your development time if you use Flash/Flex for your control panel, so from that standpoint I would strongly advocate it. You may also be able to influence your customers' environments if you are adding highly valuable features, so the objection may disappear if the value is high enough.
However the value has to be quite high for people to contemplate such a change to their working environment. This is especially true in environments who feel that Flash is a risk and have removed it because they tend to be paranoid about software on the desktop. Shorter development times is not a good argument for anyone on the commercial side of the house when faced with such trade-offs, so beware of forwarding that in a customer context as a compelling argument - it isn't.
HTH and good luck - I hope you manage to switch over, you will have a huge amount of flexibility and sizzle added to your apps.