So - who gains control of Ibaraki? Miyoshi for having more units there? Or Ikko-Ikki for having the most units there that were active in the impulse which actually saw the castle fall?
See the first sentence of the third paragraph in 2.46 on page 3. Ikko-Ikki should gain control, because they were the capturing clan.
The majority of units thing is for when an entire clan falls, as opposed to a single space (specified in the remainder of that same paragraph).