I think the answer to that is that it depends. As an example, the former owner of the Carolina Mudcats, Steve Bryant, desperately wanted to get out of the Southern League because the League's geographic footprint had altered significantly from when he brought the team to Zebulon.
When the Mudcats first started play in Zebulon after relocating from Columbus, GA the rest of the SL was Huntsville, AL; Birmingham, AL; Chattanooga, TN; Memphis, TN; Jacksonville, FL; Greenville, SC; Charlotte, NC; Orlando, FL; and Knoxville, TN. By the time he sold the team for relocation, Memphis had moved to Jackson, TN; Greenville had moved to Pearl, MS; Charlotte had moved to Mobile, AL; and Orlando had moved to Montgomery, AL. Beyond that you used to have a division with Greenville, Charlotte, Orlando, and Jacksonville to the closest team in your division being Knoxville. Combine that with MLB placing greater demands on MiLB affiliates with regards to travel and rest days, you can bet Bryant wanted out of the SL and when opportunity came knocking to sell the Mudcats to Pensacola and turn around and purchase the Carolina League Kinston Indians, you bet that's what he went for. Sure his valuation dropped, I'm sure, but it was offset by losing the headache of having to be in the same division as Chattanooga, Huntsville, Jackson, and Tennessee.
Similarly, I'm sure some owners in the SAL were perfectly fine seeing Bowling Green and Lake County ceded to the Midwest League and wouldn't mind a new mid-Atlantic based low-A league cropping up to lop off having to go to Hagerstown, Delmarva, and Lakewood. Or some massive sea-change like some free-flowing of franchises between the Carolina League and the Sally League. It might be more difficult and require some redoing of PDCs, but wouldn't it make more sense to have the NC, SC, and GA low-A and high-A teams in one league? I doubt there'd be much movement there in franchise value, but again, wouldn't it be more sensible?