We have stated that the Halacha is according to J, as opposed to E. The case is similar to the case of Beit Hillel and Beit Shammai. Beit Hillel ruled only after considering Beit Shammai, and therefore the Halacha is according to Beit Hillel. However, if you are looking for the absolute truth of a matter, consider Beit Shammai.
Is it not strange that such differences of opinion exists between J and E? Is it not a sign that Yetziat Mitzrayim and the wanderings through the Midbar did not happen? My answer is that of course "it happened." However, the differences of opinion do point to something. Yetziat Mitzrayim happened to (ancestors of) E, and the wanderings through the Midbar happened to (ancestors of) J. And the ancestors of E were different from the ancestors of J!
In other words, if you are looking for the historical truth of Yetziat Mitzrayim, look in the sources of E. If you are looking for the historical truth of the wanderings through the Midbar, look in the sources of J. You have to look deep, though.