I'm a very fresh DM with about 20 hours of actual DM time and was thinking of adding the scroll of Legend Lore to a shop within my campaign for my players to use how they would like. My only concern is how the spell is stated for its use of "gives a brief description of the significant lore", might be used on the BBEG's legend for them to discover way too early that the story that's told by most everybody in the campaign is a lie. Would I as the DM be able to hint at the legend being a lie instead of giving the full true legend.

As the DM, it's fully up to you what information should be provided when someone casts Legend Lore. The information does have to be accurate, but it's allowed to be figurative, vague, or misleading.

That said, it's a 5th level spell, so player characters won't generally have access to it until they're 9th level at least. Giving them a spell that powerful in the form of a scroll much earlier than that might be asking for trouble.