Not only was the scale of warfare (the literal number of men involved) seemingly much smaller but instances of major atrocities seem much less frequent than in most other regions or periods.
An example being the willingness to ransom valuable captives instead of executing them. Another being the seeming lack scorched earth tactics seen in both Asia, and antiquity.
European war was certainly bloody and violent, but am I wrong to think that it was remarkably less brutal than most other large scale warfare in human history?
Due to the amount of time the medieval period covers, as well as the variety of cultures, religious and social classes involved, this is not an easy question to answer. On top of that, whereas the size of forces is quantifiable, it is less easy to do so in terms of brutality. However, your examples give us a comparison to work with.
The sources I use in what follows are all from what today is the Netherlands, with a focus on the military exploits of the County of Holland and the Bishopric of Utrecht and their respective opponents, both territories belonging to the Holy Roman Empire. This ensures that these army sizes are on a relatively small scale compared to what their sovereign contemporaries could field, i.e. the kings of France, England, as well as the Holy Roman Emperor. Concerning the conduct in warfare, it is safe to draw parallels between all these territories, as long the social classes involved on either side are mirrored as well, i.e. nobility versus commoners.
First, the size of armies. The size of the forces involved in a committed engagement (I'm not counting skirmishes) could differ from as few as barely a hundred, to battles between thousands or tens-of-thousands of troops, depending on the exact period; from the 14th century onward, many feudal territories in Europe were able to field relatively considerable armies. Large scale armies were prevalent in the Byzantine Empire and the Islamic caliphates such as those of the Abbasids and Fatimids much earlier than that, with a likewise sizable logistic apparatus to support them.
In feudal Europe, the size of an army would also differ with the nature of the engagement: where a levy raised for an offensive military campaign could already be quite large - depending on the strategic goal and expected resistance - in the case of an invasion by a foreign force, many feudal territories had the version of a home guard (Dutch landweer, German landwehr) in which every person who could hold a sword was obliged to do so, increasing the size of the forces considerably.
In order to give an idea of what the expected size of a forced raised to assist an ally or coalition partner could be during the late 13th century - even when provided only by a county, a relatively small territory - we have this information from one of the proposed versions of a treaty eventually established between Flanders and Holland that details in what manner the Count of Holland had to aid his Flemish peer in the case of French aggression:
...cum quingentis equitibus, tam militum quan seriantorum, et cum decem milibus peditum.
"...with 500 horses, both knights and squires, and with 10,000 foot soldiers."
^(Proposition of the February 1298 treaty between Gwijde of Flanders and Jan of Holland.)
This means that even on the level of a county - which in this specific case admittedly saw a steep rise in population and urbanization in the late 13th century - it was considered realistic to send a force of more than 10,000 men to assist in a foreign war.
If we look at warfare internal or approximate to the owned territory, when the logistic distances are shorter and therefore easier to maintain, it's clear that sizes of forces can grow accordingly. In 1345, from the 8th of June until the surrender on the 24th of July, Count Willem IV of Holland besieged the city of Utrecht. Depending on the source, the size of the forces is given as 29,000 men, 32,600 men, or 150,000 men. While the last estimation has to be written off as an exaggeration, the other two have been cross-referenced with accounts and balances that detail the purchasing of the foodstuffs for the besieging force before and during the siege:
^(Figures from Oorlog om Holland 1000-1375, de Graaf, 2004)
At a rate of 1 kilogram of food and 0.5 litres of beer or wine per individual per day (an amount that has been established through comparison with the rations of Roman soldiers as well as soldiers in the Netherlands in the 17th century), the result is:
(18,855+15,223) ÷ 1 = 34,078
17,357 ÷ 0.5 = 34,714
^(Figures from Oorlog om Holland 1000-1375, de Graaf, 2004)
Which means that it would have been feasible for this logistic apparatus to support an army of roughly 34,000 troops. If we account for proportionally more rations to go towards the nobility, as well as relatively more luxurious rationing for the common man, the sizes of 29,000 and 32,600 are still very probable. This does not prove beyond doubt that these sizes are indeed accurate, as we lack any primary sources to corroborate that, but they would have very much been realistic.
Apart from the armies mobilized by the superstates of Antiquity, such as the Roman and Persian empires, these numbers aren't any smaller than what would be fielded in an area comparable in population and size in that time; in the battle of Plataea, which united multiple of the most sizable poleis in all of Greece, the numbers of the classical authors have been around 100,000, which is most likely an exaggeration and concerns a pitched battle with the survival of these poleis in the balance. As such, the scale of warfare was not necessarily smaller than in Antiquity, depending on the period and military situation.
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