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Jefferson did NOT build the U.S. naval ships you are referring to. In fact, he was strongly opposed to building them. The naval ships that fought in the Barbary War were built during the Federalist administrations of Washington and Adams - Jefferson’s political enemies.

Dear Sir … I ask a fleet of 150 guns, the one half of which shall be in constant cruise. This fleet built … will cost 450,000 pounds sterling. It’s annual expence is 300 pounds sterling a gun, including every thing: this will be 45,000 pounds sterling a year. … Were we to charge all this to the Algerine war it would amount to little more than we must pay if we buy peace. But as it is proper and necessary that we should establish a small marine force (even were we to buy a peace from the Algerines,) and as that force laid up in our dockyards would cost us half as much annually as if kept in order for service, we have a right to say that only 22,500 pounds sterling per annum should be charged to the Algerine war. - Thomas Jefferson from Paris in a letter to John Adams 1786 on behalf of appealing to the Continental Congress for consideration).

Also, your are confusing commissioning per certain instances with the establishment of standing armies (That was constantly leading to drawn out wars, especially in Europe). Of course you conveniently forget that Adams promoted paying the bribes. As you can see from the letter, Jefferson long-standing solution was eventually solving that situation through force which he ordered during his presendency.