First off, the 'conquest of Mekkah' began when one of the members of the Quraysh Confederacy breached the Treaty of Hudaybiyyah by attacking a tribe allied with the Medinans and Muslims. Initially, the Prophet requested blood money to recompensate for the attack, termination of alliance with the tribe that had transgressed and, of course, the nullification of the treaty entirely given that the Confederacy was likely not going to comply with any promise moving forward.
Second off, there is the matter of progressive revelation and you are dismissing the first half of the Prophet's history where he stayed in Mecca and was harassed day in, day out. He preached Islam for 13 years before God commanded him to make pilgramage to Medina because the disbelievers had opted to surround his house and try to kill him.
Third, Islam is a religion that first and foremost is a reminder to humans and Jinn of their duties to their Creator. God placed us on this Earth as a test, and having a sapience is apart of that test.
Righteousness, justice and truth do not come to fruition on their own, they must be enforced. It should be reminded that God is Self-Sustaining and that anything we do on Earth does not deprive him the least. We seek to do good and cleanse corruption to please him, and apart of that is through action, words and then moving one's own heart.
As for God Himself taking action, he has already done so by Mercy when he sends Prophets from amongst the people to lead them back into the Path of Good. However, when people still refuse and are set in their stubborn ways, then God removes them so that they do not spread their corruption further.
We do not see such things happening before our eyes anymore because Allah willed it so that Prophet Muhammad is the Messenger for all of the tribes and nations in his time and moving forward. There are no Messengers after Muhammad (PBUH), it has been decided by Him and we have no say on the matter.
And to close this, it is important to read into the rules of warfare set by God. Surah Al-Baqarah, Sentence 190-194, Sentence 216 of Al-Baqarah, along with Surah Al-Ma'idah Sentence 33-34 should prove relevant to you.