Do you know which test you were given?  There may be other reasons you may experience low vitamin D levels so it is wise to discuss the issue with your physician if you are concerned.

In the realm of IBD it is pretty common to note patients who have vitamin D deficiencies.  Up to 68% of Crohn's patients have vitamin D deficiency according to the Crohn's and Colitis Foundation of America.  This could be due to various causes. 

One cause could be the lack of dietary sources due to restrictive diets implemented to lessen IBD symptoms.  Another cause for low levels of vitamin D could be issues with absorption.  This might be your problem since you report normal intake and sun exposure.  Active inflammation in the small intestine or the use of corticosteroids can decrease the body's ability to absorb vitamin D (along with other vitamins and minerals).  It may also be less easily absorbed than water soluble vitamins due to fat malabsorption. 

It is good to hear that your calcium and bone density are normal.  That does not mean that you don't need to worry about the vitamin D deficiency though.  Over time, if not treated, it could lead to issues with your bones. 

Your doctor was right to warn you that the body needs the vitamin D to utilize calcium properly.  Has your doctor discussed the use of a supplement?  Supplementation needs to be monitored by your physician to prevent causing hypercalcemia or toxicity. (Though this is usually seen only in patients given extremely high doses).

The National Institute of Health has a list of good food sources of vitamin D here.

There is a lot of research going into the role of vitamin D and autoimmune or inflammatory bowel disease (Here) and Health Central also posted an article recently about it's role in colorectal cancer.  Obviously vitamin D is an important substance and getting a treatment plan to resolve your deficiency is something you need to discuss with your physician.

Your question about whether or not your seemingly normal calcium level will wind up  too high if you start supplementing with vitamin D, is a good one, MERF. (Not everyone is aware of the important relationship between vitamin D and calcium to our bodies, so you are way ahead of the game! )

But, the relationship is not as simple as it may seem...

Vitamin D deficiency causes a decrease in ionized calcium in blood. This leads to an increase in the production and secretion of parathyroid hormone (PTH).

PTH stimulates the mobilization of calcium from the skeleton, reduces loss of calcium from the kidneys, and causes increased excretion of phosphorus from the kidneys. The result is a normal fasting serum calcium, and a low, or low-normal, serum phosphorus.

So, vitamin D deficiency is characterized biochemically by either a normal, or low-normal, serum calcium with a low-normal, or low-fasting, serum phosphorus and an elevated serum PTH.

You will not wind up with too much calcium in your bloodstream by receiving the needed vitamin D, because, right now, your vitamin D deficiency is causing a cascade of hormonal activity that is taking calcium from your bones in order to maintain a chemical balance in your blood-and, you sure don't want this "borrowing" of calcium from your bones to continue!

Be well-

Hope