Definitely.Would you send your husband/wife away not to become illegal knowing that he/she is eligible to file for AOS being illegal?
Besides the fact that it is improper, nothing is guaranteed. Suppose the OP's wife get into an auto accident while being illegal. They check her immigration status and start a removal proceeding. A slim chance but possible nonetheless. Never mind that she won't be able to travel to her home contry when she has a family matter to attend to. Never mind that she can't work. Never mind that she will be afraid to call police when she gets harrased by a stranger. And so on. And so forth.
If we use your logic, it is OK to jump the border, come into US without inspection, and marry a US citizen, which allows you to file I-601 waiver. The law allows it, right? Is the goal using any means necessary to gain immigration status?