If your network users are using your filtering DNS server, Chrome should continue using that server, and DoH should not break the filtering. Chrome would only upgrade DNS to DoH if it could do so to that same filtering DNS provider.
If you are intercepting or blocking DNS requests to filter requests sent or attempted to be sent to any other DNS server, then you may need to ensure DoH is disabled for the filtering to keep working. In the current experimental state of Chrome DoH support, DoH is automatically disabled if any group policies are set in the ADMX files. We are working on adding group policies to specifically control DoH, and the current plan is for those settings to also default to disabling DoH if there are any group policies configured. So I suspect you are likely already done with what you need to do to disable Chrome DoH.
And it is always good to keep in mind that malware often will not use Chrome or respect Chrome's configuration in resolving DNS. Chrome can only control DNS requests made by Chrome.