Methadone is used with many thousands of patients, most of whom do not have a problem. I have not seen any evidence that it is medically necessary or appropriate to have somebody go inpatient to have their initial methadone dose set, and I doubt that many (if any) of the deaths you reference relate to an inappropriate initial dosage.
The biggest problem with methadone is that it is too easy to abuse. Some patients lie to get a greater dose than they need, or trade it for other drugs. Some use benzodiazepines or other drugs or alcohol to boost the effect. Some continue to abuse opiates while taking Methadone. The vast majority of injuries and deaths will relate not to methadone itself, but to patient non-compliance and abuse of methadone and other drugs.
Requiring daily visits to a Methadone clinic is unnecessary for most long-term patients, disrupts the ability of patients to obtain and maintain employment, and wouldn't stop abuse. Further, for a recovering addict, the Methadone clinic itself can become a risk to recovery, as I doubt that there is a Methadone clinic in the world where some of the patients aren't also drug dealers, or where some don't happily share with others information on how to smuggle methadone out (even in liquid form), or get high while on methadone.
As you note, Methadone can be the drug of choice for treating certain chronic pain conditions. Within that context, although the physician must generally apply for periodic waivers, the Methadone is typically prescribed in an office setting and not through a Methadone clinic.
Although it has a set of problems of its own, and is much more costly, many addicts will be much better served through maintenance on buprenorphine (Suboxone, Subutex, etc.). Suboxone is buprenorphine combined with Naloxone, so it is difficult to abuse. Due to the lower risk of abuse, it can be prescribed out of a regular medical office instead of a Methadone clinic.

