I don't think there is anything sinister about the name of Willoughby's estate. Both elements of the name are quite normal in English place names.

"Combe" is a very common component of English place names, and means a narrow valley. There are many of these here in Somerset where I live, including Burrington Combe and Monkton Combe.
Spelling variants include 'Comb', 'Coombe' and 'Cwm'(Welsh).

"Magna" is Latin, and means 'big', or 'large'. Whilst not as common in place names as "Combe", it isn't particularly unusual. Examples in Somerset are "Chew Magna" and Marston Magna.

Sometimes there are two places in a locality, one called "Someplace Magna", the other called "Someplace Parva". "Parva is also Latin and means 'small'.

Somehow I doubt that Willoughby would have chosen the name "Combe Magna" for his estate. The Latin element suggests to me a past association with land owned by the church, or a 17th century gentleman wishing to advertise his status as a cultured individual, though I don't have good evidence to support this. A late example of the use of Latin words in place names is "Weston Super Mare" in Somerset, which gained the suffix "Super Mare" in the 1830s when Weston was developing into a seaside resort. I suppose they thought it sounded smarter than "Weston on Sea", and hoped it would attract a wealthier class of holidaymakers to the town.