OTOH, pigs, IIRC, were also what gave Mesoamerica a pretty population boom post-Spanish conquest IOTL(correct me if I'm wrong though). But then again yeah due to 1)most likely primary aim for the muslims would be for trading, and 2) hence much less likely to occur, compared to the Europeans IOTL to see the muslims using deliberate tactics of spreading their diseases to decimate allegedly bothersome native population, or at least much less often they will be doing so, thus the Old World diseases won't be hurting them ITTL as much as IOTL, though it'll still be quite hurt. But there are still more of them(the natives) here compared to OTL, and more abundant and diverse food resources for them as well....
I think that, as long as the muslims won't be anything like the Almohads, then I agree. Then again, the Amerinds will be stronger ITTL anyway, so the damaged won't be as bad as their encounter with OTL Europeans.
Maybe, MAYBE we will see somewhat less tolerant general attitude from the muslims compared towards to the Pagans in the Old World. The New Worlders after all, still won't be as advanced as, say, India(which during this time was maybe one of the most advanced region on the globe. Remember that even if Mahmud Ghazni did destroy and pillage and plunder Hindu and Buddhist temples during his adventure, he still admitted the Hindus and Buddhist into dhimmi status.), and that they will be quite alien to the muslims. OTOH, the muslims will encounter abundance of exotic commodities, and so will the natives will find such from them. Based on what happened in Indonesia, I would think that the same pattern will apply here as well : the more a certain group that encounter the muslim traders depending themselves on trade(especially sea trade) as their main source to maintain their economy and living compared to on agriculture, the more vulnerable they are to Islamic influences.
The groups that are more into trade-relying economy will then be witnessing the advantage of converting to Islam, maybe by slowly, but surely. If we will then discuss the possibilities of Islamic attrocities in the New World in the future, they will mainly be coming from these native converts, I suspect.
But even if Islam will be mostly spread by trade, I don't think it'll be all pushing it to assume that there will be political advancement done by the foreign muslim new comers in the New World. But I think we have already discuss it, then even in the normal case(OTL still-native New World), Islamic colonization there will not be as fast as OTL's case of European colonization. ITTL's case where the natives are generally more advanced, double that at least. Also, ITTL we will see, related to the point of Indonesian Law of Islamization, many groups that basically are analogue to the Javanese abangans, springing up here ITTL Americas. Some of them are, I think, bound to be quite wilder in fact....
And all those points I've made above, doesn't include the possibility of this MR+BANW New World already developed at least one exclusive, evangelical religion prior to the dawn of Islam in the area....