Short answer: TurboTax is handling it correctly, in reporting it as two separate pieces (the $2,000 ordinary gain on Form 4797, and the $5,000 capital loss on Schedule D).
Technical explanation: Internal Revenue Code (IRC) Sec. 1001(c) provides the general rule that you have to recognize gain or loss on the sale or exchange of property as income.
IRC Sec. 1221 defines certain assets as capital assets. IRC Sec. 1222 defines capital gain as the gain from the sale of a capital asset, and capital loss as the loss from the sale of a capital asset. By implication, the gain from property that is not a capital asset is not capital gain (that is, it is ordinary gain).
IRC Sec. 1211(b) provides that net capital losses (i.e., capital losses in excess of capital gains) can offset only $3,000 of income that is not capital gains (i.e., can offset only $3,000 of ordinary gains or ordinary income). Any capital loss in excess of that can be carried forward to future years under IRC Sec. 1212(b).
The "hot asset rules" of Sec. 751 provide that a certain amount of the proceeds from the sale of a partnership are treated as proceeds from the sale of assets other than capital assets. Under the definitions discussed above, this means that a portion of the gain is not capital gain/loss, but ordinary gain/loss [almost always ordinary gain, not ordinary loss]. The MLP will do most of the calculation for you on the "sales schedule" included in your K-1 package, so that you can determine how much capital gain/loss and ordinary gain/loss you have (exactly as you laid out in your example).
And as explained above, because of IRC Sec. 1211(b), any capital loss can offset the ordinary gain only up to $3,000. Moreover, because the capital gain/loss and ordinary gain/loss have different characteristics, they are reported on different parts of your return (Schedule D for the capital gain/loss, Part II of Form 4797 for the ordinary gain). Any ordinary gain on Part II of Form 4797 will then flow to line 14 of your 2009 Form 1040, while net capital losses up to $3,000 will flow from Schedule D to line 13 of your 2009 Form 1040 and be available there to offset your other income.
As you mentioned, the sale of your entire interest in an MLP will also release any ordinary losses that have been suspended under the PTP passive loss rules of IRC Sec. 469(k)(1). These will be reported on Part II of Schedule E and flow from there to line 17 of your 2009 Form 1040.