SSIS - XML with row delimiter to a single column of a SQL table
In the flat-file connection manager, in the General pane, there is an option to set a text qualifier. If you set this to double quote (") for your file then SSIS should ignore any row delimiters that are contained between the double quotes.

There is also an AlwaysCheckForRowDelimiters property that could help. See this msdn page for more.