I have heard about Karma Vipaka, a scriptural text that mentions the consequential effects of the offenses we commit. One such misdeed is if we consider that Siva and Emperuman are the same, we beget blood-related disease; how to understand this from the Srivaishnava perspective and what are our elders’ justifications on this?

We need not refer to all the texts. We shall refer only to the texts that are provided as a source by our Purvacharyas. Superior texts like Manusmriti can be referred to. The rest are stated by devotees for Saivites. We need not consider them.
It is stated that one should not think Siva and Emperuman are the same is correct, and we do not consider them to be one because Emepruman is the supreme Lord. To understand who is supreme, there are superior texts like Srimad Ramayanam, Manu smriti, Yagnyavalkiya smriti, etc. as the proof provided by the great saints.
The rest are claims made for the respective devotees and not for us.