The modern ethnic and religious makeup of Spain (and Portugal) has little to do with the Reconquista but rather with the events that happened once it was over. Those Jews who would not convert were expelled from Spain in 1492 and the Muslims were forced to convert in the early 1500s. For more details you may want to start with this [thread] (https://www.reddit.com/r/AskHistorians/comments/4vrvw5/after_the_reconquista_how_likely_was_it_for/) where /u/drylaw talks on the events of 1492 and later and I give some earlier context.

But all of this happened once the Reconquista was over, in a period I don't really feel comfortable talking about as it's outside the scope of my studies. (Paging /u/Itsalrightwithme and linking to this [thread] (https://www.reddit.com/r/AskHistorians/comments/5lx21v/what_happened_to_the_muslims_in_spain_after_the/) for more details).

Now, during the Reconquista things were pretty different from what you seem to imagine. Both Christian and Moorish kingdoms were fairly diverse, with Muslims and notably Jews occupying positions of high authority in Christian states, for example. To quote Francisco Márquez Villanueva, medieval Christian (and Muslim) polities in the peninsula exhibited 'a de facto tolerance that had nothing to do with the modern concept of liberalism, but rather with the practical necessity of group cooperation to avoid ethnic violence and chaos' [1].

To put things into context, here's a very brief outline of how the situation changed over time. A handful of Arabs and Berbers arriving into the peninsula in the early 700s had to deal with a large Christian and Jewish population that was allowed to continue practicing their religion in return for the payment of a special tax, the jizya, that was seen as the price of their status as dhimmi, protected minorities (majorities, really). Over the course of the next centuries there was a slow process of opportunistic conversion and acculturation that led to a sizeable part of the population converting to Islam and switching to Arabic. This was sped up, from the 1080s onward, by the arrival of the Almoravids and the Almohads, fanatical Islamic sects turned into warring empires, from Morocco and beyond. Who actually entered the peninsula in direct response to Christians finally starting to take over the divided Muslim polities. The arrival of the Almoravids caused, among other things, a mass exodus of Andalusi Jews into Christian kingdoms of the north and to Provence (and, incidentally, to the emergence of the medieval Kabbalah as we know it).

Now the Christian kingdoms in the North were largely Muslim-free for the first few centuries until the Caliphate fell in the early 1000s and they could finally start their southward expansion. We are not exactly clear on the earlier stages of that expansion. There were, however, isolated incidents of mass violence like the slaughter of the local population at the capture of Barbastro in 1064, perpetrated by Aquitanian and Burgundian troops. But then again, we know about this exactly because it was an exceptional thing, done by outsiders, whereas Iberians on both sides of the religious divide were much more accommodating of each other, as often allying against common enemies of both faiths as fighting each other. (Note that we're talking about the times when the idea of crusades and religious warfare emerges in Christian Europe).

However, in the 1080s, once Christian finally start taking over cities and large areas with a sizeable population that is mostly Muslim by that time, there are no mass killings or expulsions. Here's a lengthy [writeup] (https://www.reddit.com/r/AskHistorians/comments/5idk95/were_there_muslim_minorities_in_the_christian/) of the early stages of that process that I did earlier. If I may quote myself, rather than try and conquer by force, Christian rulers now negotiate surrender. And they have to make sure the local populace stays in place and continues to produce. So Muslims who were offered and accepted clemency and surrendered peacefully would become King's Moors (or Mudejars, as we call them now), a protected group who kept their Sharia law, institutions and the use of their Friday mosque (at least for the first year after the surrender). They were relocated outside of the capital cities, though, oftentimes settling in 'Saracene neighbourhoods' right outside the castle. Note that even if both Muslims and Jews lived in separate neighbourhoods, the aljamas, juderías or morerías, depending on the local usage, not everybody did so. We do know of people living among the Christian newcomers.

Anyway, starting in the late 1000s, free Muslims were the bulk of the population in the Christian Iberian kingdoms. Some did emigrate to Muslim-ruled lands or converted over time, much like the Christian and Jewish minorities had done in Al Andalus. But most stayed Muslim (or Jewish). There was a wave of anti-Jewish pogroms that swept the peninsula in 1391 but all in all Jews enjoyed better conditions in Iberia that they did anywhere else in Christian Europe at the time. Reading late 1300s French sources at times gives you an idea in France they thought everyone in Iberia was a Jew anyway, slimy pests who only come to Paris to steal things from decent Christian folks.

Anyway, for several centuries until the Reconquista was finally over in 1492 Christian kingdoms in the peninsula had sizeable Muslim and Jewish population. As Villanueva puts it, whereas the rest of Western Europe saw itself as a society divided into three orders or estates (those who fight, those who pray and those who do all the manual work), Christian Iberia may be seen as a society divided into three religions, laws in the parlance of the times, 'in which each group assumed, loosely, a different socioeconomic function. With the Christians fully devoted to arms, the Mudejars took on industrial tasks and the most productive agricultural jobs (irrigated crops), and the Jews assumed responsibility for scientific learning, administration and the economy' (Ibid., P. 40). In particular, Iberian Muslims dominated arts and crafts, with local Christian rulers and prelates often adopting some trappings of the Andalusi civilisation that was still seen as [culturally and artistically superior] (https://www.reddit.com/r/AskHistorians/comments/5gdg8c/theres_a_rich_heritage_of_arabic_architecture_in/) long after Al Andalus ceased to be a military or economic power to reckon with.

Things did change once the Reconquista was finally over in 1492. But for the period you're interested in the answer is no. There was no intent to destroy a religious group that was clearly seen as a constituent part of the society.

[1]F. Márquez Villanueva, On the Concept of Mudejarism, in: The Conversos and Moriscos in Late Medieval Spain and Beyond. Vol. 1, Departures and Change, ed. Kevin Ingram. Leiden, Boston, 2009. P. 15. It is a shortish article that I recommend to anyone looking for a good introduction to the subject. You can read it via Google books.

Thanks for the in depth answers! I thought I might have been approaching it anachronistically but I wasn't sure and didn't know enough about the demographics of medieval Iberia to make a call definitively.

Further question if possible. Can it be considered as an early example of total war? The was a strong element of ethnic and cultural pushback by a revanchist Catholicism.