Path MTU discovery does not handle this case.
In IP, all nodes on a broadcast network must agree on their MTU. I'm not sure that's written down in any one standard, but it's definitely part of the design. Many protocols, such as OSPF and IS-IS, actively enforce this rule. In practice, if you attempt to mix MTUs on a broadcast domain, it won't work.
It's theoretically possible to create a homogeneous L2 broadcast network running IP with some jumbo-capable nodes and some jumbo-incapable nodes, if every jumbo-capable node has a static route with a MTU/MSS override configured for each and every jumbo-incapable node. All it takes is one error, however, and you have two nodes that can't talk with each other reliably. Don't try this in any production network, it's a nightmare to debug.
If you want to mix jumbo-capable and jumbo-incapable nodes, you need to put them into separate L2 domains (e.g., VLANs and IP subnets) and you need to stick a forwarding device between them (L3 switch or a real router). Then that device can return ICMP too bigs / fragment as necessary so that nodes can talk.
Oh, and two gotchas to consider.
First, there's no standard for exactly what sized frame jumbo-frames means. On some equipment, it's an on/off switch, and you are stuck with whatever value the vendor picked. On other equipment, you can configure any number greater than 1500 and below some limit the vendor picked. So you need to configure everything explicitly to ensure that they're using the same jumbo frame size, or you end up into the mixed capability problem again. (oh, and exactly what number you pick can wildly affect performance of some of your equipment, for extra fun)
Second, Windows's path MTU discovery implementation is broken. If there's any Windows in the mix you're going to get to learn about this the hard way.
Now, don't get me wrong. Jumbo frames are a very good thing. But the IEEE really let us down by taking a philosophical stance against standardizing them in 802.3z or somewhere else in 802. Much of the pain involved with using jumbo frames wouldn't be a problem if the IEEE reps did the right thing. Perhaps someday in the future they will. I hope that somewhere in the 20G/40G/100G development that more vendors get with the program to get PPS rate requirements under control.