We did build a new magic system for Thieves' World in the Player's Manual. Admittedly, it uses the standard PHB spells (with several exceptions), but the mechanisms behind it are new. We "could" have built a new magic system from scratch much like we did for Black Company but the approach I took with TW was very different for what I feel were for good reasons. In BC, there was just one author. While Mr. Cook very likely did not have hard and fast rules underpining his magic system, it was consistently freeform. BC had to reflect magic's fluid qualities.
TW, however, didn't have just one spellcasting system. It didn't even have three. Every author who ever penned a TW story that featured magic (and there were many) brought his or her own sensibilities about magic to the setting. This continued for 12 books. Long time fans of the setting and gaming can tell you that in the TW boxed set from Chaosium back in the day didn't include a magic system since it provided the essential components of the setting and then a catalog of characters interpreted by the leading game systems of the day. It had stats for the same character something like eight times or so and while some of the sections included suggestions for adapting magic to resemble the books, none were expansive in their system overhauls to accomodate TW. Take the Traveller stats where characters had a Magic stat with no instruction on what the stat meant!
Everything changed when Lynn Abbey returned to Thieves' World in the novel Sanctuary. To knit everything together she established a basic system of magic that involved acquiring magical energy through one of three basic techniques: magic, witchcraft, and prayer. Though the techniques for drawing the energy varied, the essential process remained the same across the board. The idea of a mana based system (which is what the TW PM includes) allows there to be varying levels of latent energy. When used in excess, the energy diminishes, making spellcasting harder. If left dormant, it repairs itself and spellcasting becomes easier.
We established how magic worked mechanically, but the question then fell to what spells we would include. We could have gone with a freeform system from BC, but time and again we see spellcasters studying "spellbooks" or old texts. Rituals were "fixed" entities in the TW setting and could be cast in the same way over and over again so long as all the conditions were met. The examples even extend into to the new series with Heliz Yunz who drew words of power from books and scrolls.
Another factor was the understanding that Thieves' World had long been a Dungeons & Dragons' fan city. Most old school gamers know all about Thieves' World and I've known many people who've dropped Sanctuary into their own games. So linking D&D to TW became a priority, but I refused to fall back on the Vancian system. What resulted was a compromise. It presented Thieves' World as a d20 interpretation, much like the old boxed set did, but also provided expansive rules modifications to enable gamers to bring the setting more in line with the source material.
Soon after we completed the Thieves' World Player's Manual, I had to tackle the mammoth Shadowspawn's Guide. I knew we'd fill the book up with setting info, guidance on the TW feel, a full spread of characters from both eras, and a few new crunchy bits to expand the game, but I also felt that while the magic system in the TWPM best captured the sense of the magic in the world, I worried that players who have a Sanctuary in their established campaign setting would resist altering the mechanics of magic. And so SGTS contains a section on magic that brings the spellcasting system a step closer to the Vancian system, while also injecting necessary mechanics to keep it clearly TW in flavor. This way if you wanted to bring the Warlock from Complete Arcane into TW you could without any rules clashes. In short, SGTS offers Sanctuary as a city you could theoretically drop in any setting from Kalamar to Freeport to Greyhawk to Black Company to Red Spire Press' world to Ptolus to Arcanis and yet still keep the feeling of TW the same.
So, the short answer is this: We did both. We kept as close to the Thieves' World setting as we could while still making it the D&D setting that so many DMs have made it over the years.