If she isn't seeing a GI yet then I would suggest she get referred since the differential diagnosis for diarrhea is huge. Adding in joint pain makes me think a rheumatologist may also be needed to rule out other autoimmune disorders like Lupus (can affect the intestines). Or she could have more than one thing going on. That's why the doctors make the big bucks - they have the training needed in situations like this.
From the point of view of screening out IBD, while it is possible to have CD and have nothing abnormal, it is not typical to have NO abnormal lab values. Usually there are at least some abnormal levels. The labs that are usually abnormal are:
ESR - high
CrP - high
Platelets - high
Albumin - low
Ferritin - low if there is blood loss; may be high if there is inflammation
Hemaglobin - low
Hematocrit - low
WBC - high, specifically lymphocytes and monocytes (absolute counts or % or both) are likely to be high
RBC - low
An occult blood test of stool should be done
If there are no abnormal lab values she is probably going to have trouble getting any further invasive or extensive testing done - things like an MRE or SBFT. But it will depend on the GI and the particulars of course.
Running the Prometheus IBD testing is another option but it is expensive and not always conclusive. However, it's very unlikely that a high level of certainty on this test would be a false positive. That means that if she tests positive for CD (UC is pretty much ruled out by a normal scope) and the test finds a HIGH likelihood of CD then it is probably not wrong.
Other possibilities that come to mind:
I agree that celiac should be ruled out - while upper endoscopy is gold standard there are very reliable (although not perfect) blood tests that can be used for screening. If she has celiac of long standing there would likely be other systemic symptoms that could be identified.
There could be SIBO - bacterial overgrowth - contributing. If this is suspected then Xifaxan ($$$$) could be rxd to see if it helps symptoms along with use of probiotics.
Fat malabsorption presents with diarrhea most of the time but, again, there would almost certainly be abnormal labs and other findings that made the GI suspicious about this possibility. It is assessed by a special diet with stool sample collection over several days time.
C. diff should always be ruled out, if necessary with 3 consecutive samples done using the longer test.