Using some creative substring, float, and charindex logic, I came up with this:
delete l1
from
latlong l1
inner join (
select
id,
substring(cast(latitude as varchar), 0, INSTR(CAST(latitude as varchar))+3, '.') as truncatedLat
from
latlong
) l2 on
l1.id <> l2.id
and l1.latitude = cast(l2.truncatedLat as float)
Before running, try select * in lieu of delete l1 first to make sure you're deleting the right rows.
I should note that this worked on SQL Server using functions I know exist in MySQL, but I wasn't able to test it against a MySQL instance, so there may be some little tweaking that needs to be done. For example, in SQL Server, I used charindex instead of instr, but both should work similarly.