Hi Newguest,
For a start, that sentence should really have commas around the inserted relative clause to show that the action that follows still applies to the main subject (experiment) - so:
In fact, the reactions of both groups were so intense that the experiment[,] which was to have lasted for two weeks[,] was broken off after six days.
Using "was to last" instead of "was to have lasted" sounds slightly strange to me in the new sentence. I think it is because the use of straight "was" sounds more definite, making the part that follows feel contradictory. "Was to have" shows me that it was the original plan that didn't come to pass. On the other hand, a word like "supposed" can do the same function more effectively, giving us either:
In fact, the reactions of both groups were so intense that the experiment[,] which was supposed to have lasted for two weeks[,] was broken off after six days.
or
In fact, the reactions of both groups were so intense that the experiment[,] which was supposed to last for two weeks[,] was broken off after six days.
Even there, the use of the perfect tense rings better for me in showing that it was an original planned action that did not happen, with the follow up information in simple past tense confirming the action that did happen instead.
Hope that helps,
Jason