Additionaly, the despise with which the european society would look on eunuchs would further isolate them. Therefore, they would be loyal only to the emperor and to no other party.
I'm not sure of this last assertion. Indeed, the eunuch predates medieval Christianity and Islam by millennia. Both Roman and Hellenistic cults (i.e. Cybele, but one example) featured eunuchs. Even with the marked, though not complete, decline in awareness of late antiquity during the western European medieval period, some conceptual knowledge of the practice existed even among those removed from contact with the Islamic sphere.
Certainly, most learned Christians (i.e. educated clergy), even if they had never met a eunuch, would have known of eunuchs at least conceptually from Acts 8:26-40. The Vulgate word used to describe the Egyptian eunuch in Acts 8:27 is
eunuchus (Greek
εὐνοῦχος,
eunouchos). These words are identical (Greek
ou ---> Latin
u consistent in the Vetus and the Vulgate.)
Conceptual knowledge, cultural interchange, and regard are mutually exclusive. To prove that European society despised eunuchs, one would have to first establish widespread knowledge of eunuchs in diverse European subcultures outside of mere scriptural context. There would also need to be a trace of the cultural interchange between Christian and Muslim cultures over the practice. Only then could a person assert whether certain European groups accepted or rejected the practice of castration.
Remember that the "Islamic
ummah" and "Christendom" were in quite close contact with each other from the advent of Islam.
The new eunuchs would probably be very thankful to Frederick. Also they had to loss their gonads, they would aquire positions of power and wealth, far beyond what they would have had otherwise in their lives.
This is quite possible. Parallels exist in later Ottoman society, where ostensibly Christian boys obtained from the Balkan states and Greece converted to Islam and obtained very high places within the state system. To my knowledge, janissaries were not castrated. We have excellent Ottoman scholars here at AH that can clarify the janissary process for you -- just write a question about the process.
As Frederick had access to very skilled arabian surgeons the castrations should have been just a routin procedure. Mount Aetna could have provided snow to anesthise the scrotums of the future eunuchs by cooling it down before the testicles were cut out. This could have helped to make castration less traumatic for Fredricks eunuchs.
Hippocrates and Galen both knew of more effective anesthetics such as crude opiates. The main issue with surgery in antiquity and the medieval period is sepsis. I have read that in some areas of Italy in the 17th through 19th centuries over 90% of castrated boys died from septicemia (blood infection). Frederick and his doctors would have been well aware of the risks of surgery. He and his advisors would have accounted for the inevitable deaths from castration, including shock, infection, and secondary symptoms (i.e. fever).