(Note: The answer I previously posted was not relevant to the question I now clearly see here. Unless someone changed the wording of the question, I was probably in a sleep-deprived haze.)
If by "disciples of Jesus" you mean THE Disciples who followed him during his lifetime, then they were definitely Muslim.
This, however, is in the Quranic definition of Muslim; a true monotheist who believes in one God, the last day, the angels, and all prophets of whom they are aware, such as Jesus as a prophet and messenger of God in the same tradition and religion of Moses, Abraham and his lineage, such as Solomon and David (using anglicized names), as well as the Gospel and previous revelations. Islam is the exact same religion as that of Jesus or Moses; it is not an organization one joins or a religious club with members and non-members. It is a complete system of morality and behavior, law and faith, governance and principles. Anyone who conforms to the just laws and principles of Islam, whose faith is sincere and devoted to God alone, whose acts confirm the faith and its compassion and civility and goodwill (among other qualities), is Muslim and Mu'min (faithful). The word "Muslim" is not a title but a description which means "surrendered (to Allah)". I prefer "surrender" which is voluntary to "submission" which can imply forced in English, and there is, according to the Quran, "no compulsion in religion." (Al-Baqara 2:256)
When the Quran refers to "Christians" and "Jews", the terms are what later people called themselves. Much translation and interpretation changed the Gospel of Jesus and added other books into one called The Bible. But all are one religion;
From Surat Al-Baqara 2:62:
"Surely those who believe; and those who are Jewish, and the
Christians, and the Sabians, whoever of them believes in God and the
Last Day and does good works; they will have their recompense with
their Lord, and there is no fear upon them, nor will they grieve."
This shows Jews and Christians to be of the same religion as Islam, defined by adherence to monotheism and righteousness.
From Surat Al-Maa'ida 5:82:
- "Strongest among men in enmity to the believers wilt thou find the Jews and polytheists; and nearest among them in love to the believers
wilt thou find those who say, "We are Christians": because amongst
these are men devoted to learning and men who have renounced the
world, and they are not arrogant."
This indicates the Christians called themselves this name; and shows the flip side of those who identify with these religions as so-named, that after the coming of prophet Mohammad and the Quran, many of them kept their separate faiths and rejected the prophecy of Mohammad and the Quran as divine revelation. On the other hand, the Disciples were there at the time of Jesus and were close followers, and since Jesus was a prophet of Islam, they would also have been Muslim.
As you pointed out, sometimes the Quran refers to Jews and Christians as believers and sometimes as even enemies. This is because their faith is not a matter of named religions but rather of the heart and the actions of each individual. The point about "shirk", or joining others with Allah to be worshipped alongside Him, as the Christians do with Jesus, is considered by Allah as idolatry and a violation of the first commandment. Such Christians as believe this or believe that Jesus is "son" of God are idolators and not Muslim. They can call themselves Christian but they are not in fact following the actual teachings of Jesus. Therefore such Christians are not Muslim, even if they claim to be "disciples" in the sense of devotees.
I hope this has made it clear.