Theoretically yes. It would just take rerouting the incoming kidney blood supply into a loop to bypass it into dialysis. However, you would likely have to filter the drugs out, pass it back to the kidney, reroute it out again and restore the drug. Wouldn't help if your kidneys died from lack of blood supply. Last case scenario stuff probably though.
While the idea sounds like a good idea on paper, I have to tell you, as a practicing surgeon, it really sucks.
First let me clear up, the antibiotics themselves are either directly nephrotoxic (damage the kidneys) or their breakdown products are. Its not a matter of taking the kidneys “off-line”. And in addition not all drugs are removed with dialysis.
To access both renal arteries and veins (assuming normal anatomy many people have duplicated renal vascular systems) is not an benign undertaking. The vessels are in the retroperitoneum (behind all the structures in the "classic" abdominal cavity. So it is not a "trivial" procedure. Next to totally bypass the kidneys is not a great idea...extended bypass systems tend to cause a lot of damage to the blood, they can speed up the drestructiong of red cells (oxygen carrying) and platelets (clotting cells). The circuit also tends to active the clotting system and you get a paradoxical, hyper/hypo-coagulable state. This is similar to DIC (Disseminated intravascular coagulation) [http://en.wikipedia.org/wiki/Disseminated_intravascular_coagulation]
Also the bypass circuit itself is made of synthetic material with acts to harbor bacteria. Given large scale infections, we as surgeon, routinely remove all sorts of prosthetics (AV graft material used for dialysis, artificially heart valves, pacemakers, rods and screws from orthopedic procedures)
The information in the article itself is not new. When I did a rotation in a burn unit in 2004, we had a standing problem with the unit harboring several species of Acinetobacter, and these organisms were resistant to all the antibiotics that the lab routinely tested. We routinely had to use Imipenem(tm) [http://en.wikipedia.org/wiki/Imipenem]. And it was not unusual to have bugs start to build resistance to that drug. We usually had to resort to poly-pharmacy as opposed to mono-therapy as we usually prefer.
Again as I posted a few weeks ago: As physicians we need to be vigilant in our use of antibiotics, but patients need to be respectful of them as well and to stop asking for an antibiotic (that is useless for viral infections) for every little sniffle when you have the common cold or flu (both caused by viruses).
Forgive me for quoting wikipedia, but I felt some footnotes were warrented. I usually yell at my students and residents when they quote it to me, but for the level of discussion here, it is adequate.