I have used Tor extensively in many situations and across many organizations and simply using it never "caused IDS and firewall alerts". Can you give examples?
What do you mean by "not particularly resilient", compared to other remote management solutions? Tor is very good at handling temporarily broken connections, change of networks etc. -- much better than many other solutions like openVPN.
Addresses of onion services in the current design can be discovered, true. Again, this is not different from many other remote management solutions. You can (and should in this scenario) use authenticated onion services, which means that unless you know a secret you cannot access any service behind an onion. See "HidServAuth" in the Tor manual.
"The Tor network is already over capacity" -- what makes you think that? Here's a graph roughly comparing available vs. used bandwidth: https://metrics.torproject.org/bandwidth.html