Recent research by Freitas (using the methods of computational chemistry including Density Functional Theory) examining specific reaction pathways for diamond mechanosynthesis (DMS) has hinted at the possibility that this assumption might be unwarranted. DMS appears to be extremely reliable at liquid nitrogen temperatures (~80 K).
However, there appear to be a number of competing reactions for several of the critical steps in building diamond structures that might become accessible to the tooltip chemistry at room temperature (~300 K) - the temperature at which ecophages would be expected to operate. If any of these competing pathways were taken during a DMS reaction sequence, the result would be the creation of a pathological molecular structure in the partially-completed product object (i.e., the daughter ecophage). That is, an irreversible structural error would be created during fabrication that could not be corrected, thus ruining the product object.
The research is an early release of information from this paper which is in preparation.
Robert A. Freitas Jr., Ralph C. Merkle, A Minimal Toolset for Positional Diamond Mechanosynthesis, J. Comput. Theor. Nanosci. 4(2007). In preparation.
NOTE: if DMS is made to work at liquid nitrogen temperatures that would still be huge in terms of being able to build the large scale and world changing things that we hope to make.
NOTE: Also even if the initial difficulties at room temperature prove to be non-trivial, it does not mean that they cannot be overcome with more work or creative approaches.
This is early but important work.