I've addressed this point previously. I certainly don't think that it's illogical for Guede to have staged a break-in (not that I think this is what happened). My reasoning is this: if Guede had been let into the cottage by Meredith, and after killing her he'd left by the front door (i.e. leaving no signs of a forced entry), then the police would be able to deduce with some certainty that Meredith had been killed by someone she know (or at least by someone she felt comfortable opening the door to, when she was home alone at night).
Now, the universe of people whom Meredith might have opened the door to, who were also in Perugia that night and who didn't have an alibi, is pretty small. And it wouldn't be all that difficult for Guede to figure this out. In other words, his thinking might go along the lines of: "There might be only, say, 5-10 people who were known to Meredith and who have no alibi, and I'm one of them".
Therefore, it's not at all illogical for Guede to think that he might at least dilute possible police focus on him by making it look like Meredith was killed by somebody unknown to her who entered the cottage by breaking in. Even though he had previous form as a burglar, it wouldn't be hard for him to realise that the potential universe of people who might have broken into the cottage might be considerably greater than the universe of people who were known the Meredith (and who were in Perugia that night with no alibi). After all, this potential universe for a break-in would include not only known burglars, but also most known sex-offenders, and in fact could not exclude pretty much any male between the ages of 16 and 50 who was in Perugia that night and who had no alibi.