I am normally recommend BizTalk left, right and centre, however in this case I would go with SSIS for two reasons:
On a file 50Mb plus you will get much better performance out of SSIS, no matter how many resources you throw at BizTalk given the way that BTS will process each record within the file. There are strategies here of course, but SSIS will win hands-down (Although I would imagine you web-service will probably be your bottleneck irrespective of which solution you choose); and
Unless you write a custom flat-file disassembler (which is almost rocket-science, BizTalk God territory), the standard disassembler will simply stop when it reaches a malformed line, logging the error into the Event Log and no further message processing will take place.
As an aside, I have been dropped into far too many projects where customers have a solution written in BizTalk where batch operations are being performed. The original development and testing was completed on flat-files c. 1Mb - 10Mb. Customers are then confused when a 50Mb - 100Mb+ files take so long to process!
Its much better to choose the right solution to the problem (IMHO, SSIS) at the beginning of the project, rather than crowbar a solution onto a product that isn't suitable.