This is not really a POTUS versus a state governor legal issue. Basically, Holder is saying that Kansas law enforcement cannot lawfully arrest federal agents performing federal duties even with the Kansas state statute. The authority that federal law enforcement agencies fall under is actually a result of Congressional law. In other words the law enforcement power and various jurisdictions of federal law enforcement agencies is granted and defined through federal law. Basically Holder and of course the POTUS ultimately administers these federal law enforcement agencies but their actual authority to carry out federal law comes from the legislative branch of Congress.
In practice, I doubt the federal agents would be arrested for directly violating that particular state law. The initial arrest would be for, say, DUI and resisting arrest, with the charges later dismissed.
Since the purpose of this would be to prevent them from seizing firearms, there might be a 48 hour pause in which their intended victim’s weapons would be transferred, making them no longer available for seizure.