I am not at all certain why you would assume that protolanguages must have no morphology. PIE is just a language like any other before or since. If we review the relevant article, the Font of All Knowledge explains that morphology is the study of words, how they are formed, and their relationship to other words in the same language.
Whether your language has affixes, adpositions, or some other means of distinguishing roles all of that falls under morphology. Thus, I'd argue that it is "naturalistic" to insert morphology into your protolanguage. After all, it's already there! Else, your daughter languages most likely wouldn't have the concept at all. (And that kind of speculative invented language would be very interesting indeed!)
Standard examples, consider Latin & English:
john bit the dog
the dog bit john
the dog bit john
john bit the dog
johannem momordit canis
canem momordit johannes
canis momordit johannem
johannes momordit canem
Morphology tells us how the words are related to each other. Just because English got rid of almost all of its endings doesn't mean we did away with morphology! We just tucked it away somewhere else, in this case, word order. This is why Latin can put the agent or the patient before the verb, but English, except in unusual circumstances, can not. We expect that whatever noun comes before the verb is the agent, be it the dog or be it John.
Morphology has even been proposed for Nostratic, the protolanguage from which PIE descended.