If your company mandates installation of malware, then that's not something an app store can fix. If your company mandates the installation of malware and it's not available on the Apple AppStore, do you think they'd just say, "well okie dokie I guess the policy doesn't apply to you"? No, they'd require you carry a compliant device.
If my company is mandating the installation of software on my devices, I'll request a corporate device and assume the company has root access on said device.
I'm not sure how this is relevant to my point: "sorry your app isn't on the Apple app store" probably isn't enough to stop an oppressive employer from forcing employees to install spyware.
If my company is mandating the installation of software on my devices, I'll request a corporate device and assume the company has root access on said device.