In my experience, the answer is a definite maybe. The normative reference would be the IRT Engineering Guideline, but it doesn’t have much to say about discrete converters. I see two potential problems.
1) With modern PROFINET devices, the media type of each port in the network is stated in the GSDML file. So when you create your topology, the engineering system may not let you connect a FO port to a CU port. I believe that the TIA software from Siemens will let you do this, but other engineering systems may not.
2) The line delay values of the segment containing the media converter may need to be adjusted manually in the engineering system. In the best case scenario, the media converter will have a fixed delay value and introduce no jitter at all in to the network. But it will still have some delay, and it may increase the line delay between the two connected devices beyond allowable values (e.g. greater than the equivalent delay of 100m of copper cable).
I’m sure there are discrete converters out there that will work for your IRT application, as long as it runs at fairly long cycle times ( >=250us ). But the cleanest solution would be to either use a PROFINET managed media converter, or to break your topology up in to two synchronization domains on either side of the discrete media converter and keep it out of your topology.