Multiple-input multiple-output (MIMO) transmission approaches have been recently considered in the context of molecular communications due to desirable improvements they provide in terms of communication efficiency. Among these methods, molecular index modulation (molecular-IM) schemes yield a significant improvement in throughput and show promising results for future molecular MIMO research. However, existing molecular-IM methods rely on perfect spatial alignment between corresponding antennas, which may not be the case in a possible practical scenario. Motivated by this practical constraint, this study proposes a novel receiver design for molecular-IM. The proposed decoder is an augmented version of the maximum count decoder (MCD) and operates by merging MCD with a simple linear combining technique. Our numerical results show that the proposed approach yields a desirable robustness against antenna misalignments while still maintaining a simplistic receiver structure.