I've been reading some really disturbing stuff about what is going on.
Can't stop thinking, how exactly do ISIS, persecuting 'pagans', killing those who oppose them, taking women as slaves, differ from what Muhammad and his companions did?
this is all very awkward for apologists to explain away.
This is a very interesting question. If I were still a salafi, I'd likely fault IS for using jihad as a first tactic instead of a last resort. Based on what we can gather from the seerah, the argument can be made that Muhammad seemed to have been more pragmatic than these ISIS bandits. He did not seem as interested in fighting just for the sake of fighting as these ISIS folks seem to be. He entered into peace treaties, even with the pagan Arabs, allowing him to free up his resources and build his community. He also only seemed to attack at opportune times, for example, when he stood to capture lots of booty to feed his men or when he had a great chance at successful conquer. Remember, the battle of badr was only initially meant to be a caravan raid until Abu Sufyan discovered Muhammad's plans and called in the Makkan army. Muhammad was initially considering fleeing until his men talked him into fighting.
Also, the treaty of Hudhaibiah was seemingly not in favor of the Muslims, but it freed up Muhammad to focus on conquering the fertile northern oases and recruiting more desert Arab tribes to his movement. By the time he decided to conquer Makkah, Muhammad had already won over, through skirmish and through bribery, many of the Bedouin tribes (remember, one of the permissible uses for zakat is to "soften the hearts of those who just accepted Islam," aka, bribing tribal leaders who submitted to his rule with gifts.) He took Makkah without a fight because they simply would not have been able to put up a resistance.
Muhammad seemed to have been a lot more patient and focused on achieving his long term goals. He didn't go picking fights he knew he could not win, or killing people who disagreed with him right away. Remember, he refused to kill people he considered hypocrites because he didn't want the news to spread that "Muhammad kills his companions." While he did do some really atrocious things as he captured cities, massacred men, and enslaved and raped women, he didn't seem to do these things just for the sake of doing them. He seemed to have had his end game strategy in mind the entire time and tried not to shoot himself in the foot for the sake of being overzealous.