I would tend to agree with you that in some (or many) cases the fighting along the border was not 'over slavery'.

There was a lot of hostility between different factions unrelated or indirectly related to the slavery issues. There were thieves and murderers that used existing conflicts as a cover for their activities. Jayhawkers robbed, burned houses, and murdered people in Missouri indiscriminately using the excuse that Missourians were bad people without regard to whether they were pro-slavery or not. Missouri bushwhackers raided Kansas because they were troublemaking abolitionists, as retaliation, or some other rational when their only motive was thievery. "Father Paul" at Osage Mission said men would come through that were Union men one day and Southern men the next. Jayhawkers also raided into the Cherokee Nation (in Indian Territory) to steal cattle and horses. Drew's 1st Cherokee Mtd Rifles believed their primary purpose was to protect the Cherokee Nation from Kansas jayhawkers.

As mentioned in a prior post, the error on the printed Kansas maps showed the northern boundary of the Cherokee and Osage lands 8 miles south of the actual survey line. Settlers arguably believed that land was open to white settlement. Whites were prohibited from settling on Indian lands. Some ignored this, (settling south of the 8 mile error) believing the US Govt wouldn't force them to move, which was too often true. Mathews and his followers were apparently trying to drive out these intruders to protect Indian lands but also because the settlers were anti-slavery. Watie's "battalion" was stationed in the Cherokee Neutral Lands to protect the Cherokee Nation (and northwest Arkansas) from invasion from Kansas.

To add to the complexity, the Cherokee Treaty of 1835 (Treaty of New Echota) said Cherokee lands would never be included within a State or US Territorial government (Indian Territory, present Oklahoma, didn't have a territorial government) but the US Congress ignored this and included the Cherokee Neutral Lands within the Territory of Kansas and then the State of Kansas. Prior to the war, it was recommended by the Commissioner of Indian Affairs that the Kansas border be changed to the northern border of the Osage lands and the Cherokee Neutral Lands (after purchasing the 8 mile strip from the tribes). Those in power in Kansas opposed the proposal and wanted all Indians removed from Kansas and their lands opened to white settlement.

When the Cherokee and Osage signed treaties with the Confederate States, their lands in Kansas essentially became part of the Confederacy -- and the treaty promised their lands in Kansas would not be part of a State or Territorial government. The priests at Osage Mission discouraged the Osage from treating with the Confederates putting them in conflict with their long time friend Mathews. (The majority of the Osage rescinded their treaty with the Confederates.) It seems there was also a business dispute between Mathews and Sam Gilmore, who was in Humboldt, which seems to be a factor leading to the Sept 9th raid.