I would follow through as a WC injury. FMLA would follow the WC paperwork. Let me explain using information from the January "THOMPSON Guide to the Revised Regulations."
"With FML events the first thing to do is to analyze whether a medical certification is necessary in every case. While consistency always helps avoid discrimination claims, absolute unequivocal consistency is unnecessary. Situations will arise in which obtaining the certification will not add any benefit to the process."
The situation you have presented is one of those times. If an employee suffers an injury at work that clearly will incapacitate the employee and will be covered by WC benefits, knowledge of that is enough to conclude the leave will be FMLA protected. Medical information derived through the WC compensation claim would likely provide the same information the FMLA standard would want.
So send the employee for a med evaluation under WC. If the employee is incapacitated under WC simply use the same information to assign the employee as FMLA qualified. Give the employee the completed 'Eligibility Form' which should contain the employees rights in the form. Also give the employee the required 'Designation Form' detailing how the time will be taken and when an expected return to duty will occur. Both forms must be given but both forms can be given at the same time.
Lastly it is always a good idea to send a class specification description with the employee for medical evaluation. It should contain the essential job duties assigned to the employee. Since you say that this is new to you I wonder if you have all of the forms that will be needed? If you need to view something let me know and I will see what I can do to send you my forms which are modified from the DOL forms for our company. Hope this helps.