Is there any way to sell an item valued at more than 3000 gold for its actual worth in Oblivion?

No. You are right about the limit being 3000 gold.

As a minor compensation for this disappointing answer, you can invest in a shop before you reach the Expert level by fortifying your Mercantile skill at 75 or higher.

And, for the sake of exhaustion, I have added a list of the wealthiest merchants in Oblivion GOTY:

• Aurelinwae can be found in the Mystic Emporium in the Imperial City's Market District. Once you have mastered Mercantile AND have invested in her shop, she has 3000 gold. In addition, she has a low mercantile skill (of 6) herself (meaning it's easier to sell items at higher prices). She will only buy non-magical items once you have reached skill level 50, though.

• Rowley Eardwulf, in the Wawnet Inn, west of the Imperial City, has the same amount of money (provided the same conditions are met), but a much higher mercantile skill level (of 44).

• The third and last NPC with this amount of money is Nilphas Omellian, who is a trader living at the Merchants Inn, also in the Imperial City's Market District. His skill level is slightly lower than Eardwulf's (at 40), and he will buy any type of item from you.