this is a serious case
generally new chromosome abnormalities in Ph-neg cells can be "benign" if they include things like trisomy 8 which is probably the most common. These patients should be monitored.
7q- or monosomy 7 however is bad news. I agree with Michele that you should confirm if this is clonal, ie more than one metaphase with this abnormality
We actually reported in detail the natural history of such a case a few years ago.
Ostro D, Chun K, Kamel-Reid S, Lipton JH (2007) Chromosomal Abnormalities in Chronic Myeloid Leukemia: Evidence of a Hierarchy in Imatinib Treated Cells. Leuk Lymph 48: 195-6
This patient will very likely go on to develop AML, not CML blast crisis, but 7q- AML which will be hard to treat.
You may find that stopping the TKI may allow the CML to re-emerge and this MDS clone transiently disappear, but in the long run, I expect your patient is in for problems.
I agree completely that you should aggressively pursue the unrelated donor search and if no MUD, then consider a cord if possible. Given the need for GVH/GVL with CML, I would be concerned that a haplo might be too immunosuppressive and relapse would be higher than the usual approx 40%.