We introduce a version of Khovanov homology for alternating links with marking data, $\omega$, inspired by instanton theory. We show that the analogue of the spectral sequence from Khovanov homology to singular instanton homology (Kronheimer and Mrowka,\textit{Khovanov homology is an unknot-detector}) collapses on the $E_2$ page for alternating links. We moreover show that the Khovanov homology we introduce for alternating links does not depend on $\omega$; thus, the instanton homology also does not depend on $\omega$ for alternating links.