Sort of, yes. The character of Odysseus certainly underwent a slide from a hero who was iconic of resourcefulness and exploration, in Homer, towards a cunning utilitarian, a sophist, and a malevolent villain who consistently used his intelligence for evil. That much is certainly true.
But in the mediaeval period, the only people reading the Iliad itself were in the Greek-speaking world: that is to say, the Byzantine Empire. Even in the Greek world, though, Odysseus was usually treated as a villain, starting in Diktys of Crete (ca. 100 CE) and Philostratos (early 3rd century); and one 5th/6th-century historian who treated Diktys as the definitive historical account of the Trojan War set the basis for most interpretations of the war and the characters in subsequent centuries. But that doesn't mean that Greeks were sympathising with the Trojans: the Trojans could be the heroes of the story for the Romans, but for the Byzantines they were after all barbarians, and the Greeks were the good guys. Odysseus just happened to be a bad egg.
Here's a description of Odysseus from a 13th/14th-century Byzantine discussion of the Trojan War known as the "Uffenbach Troika": the UB takes a step back from Diktys/Philostratos, and represents a return towards Homer, but on the subject of Odysseus it sticks with Diktys'/Philostratos' portrayal.
Odysseus was the son of Laertes and Antikleia, from the island of Ithake. He was clever, even to the point of being a villain, gifted at demagoguery, so that even "the torrent of his words was like flurries of snow" [=a paraphrase of a passage in Iliad 3]. He was a crowd-pleaser, and plotted secretly even against the king himself; and he was the cause of the ruin of the greatest and most admirable heroes -- Palamedes, Aias, and Philoktetes. For he marooned [Philoktetes] on Lemnos, racing away on the ships; and he murdered Lokrian Aias, who was fleeing with him by sea.
In the Latin west, the characterisations in Vergil, Ovid, Diktys, and Dares of Phrygia were definitive, and Odysseus/Ulixes was consistently treated as a monster in the Troy matter as covered by western mediaeval writers like Benoit de St.-Maures, Guido of Colonna, and others. Pretty much the one exception is from the Greek world: in Quintus of Smyrna's 15-book epic on the end of the Trojan War, dating to ca. the 4th century, Odysseus comes off very well indeed. Even in the episode of the judgement of the arms, Aias reviles him, but the narrator seems to regard Aias' criticisms as unjustified. (The criticisms are basically a holdover from Ovid's account in the Metamorphoses, where Odysseus/Ulixes is a villain, and Aias/Ajax is very definitely in the right; Quintus borrowed heavily from Ovid, but not in that respect.)
The ultra-negative view of Odysseus goes back at least as far as Vergil's Aeneid, which dwells at length on the cruelty and dishonor of the Trojan Horse deception. Of course, Odysseus was seen as a pretty morally gray character even by the ancient Greeks. The Greek language was much less well-known than Latin in Western Europe during the Middle Ages, and at least as late as the 14th century the character of "Ulysses" was better known from Roman sources than from the Illiad and the Odyssey. This is demonstrated, for example, by the portrayal of him in Dante's Inferno, which contradicts the Odyssey's ending. (Incidentally, Tennyson's poem "Ulysses" is based on the Inferno, not the Odyssey.) So the view of Odysseus in medieval Western Europe would have been pretty negative. Achilles, the actual protagonist of the Iliad, was seen in similarly negative terms by Roman and medieval writers.
As for attitudes towards the Trojans, Hector was celebrated in medieval times as one of the "Nine Worthies," and the 12th-century Historia Regum Britanniae makes the (completely legendary) claim that the British (i.e., Welsh) people were descended from Trojans, just as the Romans were according to Vergil.
All of this is about Western Europe, though. I have no idea how the Byzantines felt about the Trojan War.