This answer focuses not on the proteins but on the effects of the vitamin B12 found in Spirulina.
You can't be sure yet whether or not Spirulina is bad. There are not enough studies with consistent results to show whether the form of vitamin B12 found in Spirulina is usable.
The German Wikipedia contains some information on the effectiveness of Vitamin B12 (cobalamin) contained in Spirulina. According to the article Spirulina contains 80% unusable cobalamin which may block the absorption of usable cobalamin.
Spirulina contains an ineffective form of the vitamin ("pseudovitamin B12", "vitamin B12 analogues"), approximately 20% of which is the vitamin form which can be used by the human being, relative to the analytically determined high total value. This ratio of usable vitamin and so-called analogues is found in many, including animal foods, so it is not a specialty of Spirulina. According to a purely theoretical consideration, it is possible that an excess of analogues can block the uptake and metabolism of the physiological vitamin B12; This theory is neither proved by experiments nor by patient studies.  Studies in 1991 and 1999 with children with a vitamin B12 deficit showed that after the administration of spirulina, the blood level of measurable cyanocobalamines increased, but the symptoms did not disappear.  
(Translated via Google Translate.)
Note that the inconsistent results, showed in the study mentioned in the last sentence, are probably caused by the fact, that the blood concentration of vitamin B12 is not a reliable indicator to determine B12 deficiency:
Serum homocysteine and methylmalonic acid levels are considered more reliable indicators of B12 deficiency than the concentration of B12 in blood. The levels of these substances are high in B12 deficiency and can be helpful if the diagnosis is unclear.